Conceptually, visually and in the execution:
1. The design of the ship
I didn't really mind it being a rehash of the Akira class, but never thought it was an original or marvelous design either. John Eaves had several sketches for the NX-01 that would have been superior final products. In the end the design alienated a lot of fans from the get-go, and hurt the show.
2. The Uniforms
A minor gripe, a deeper blue, less purple, I would have added name tags and a United Earth flag and Starfleet logo. Star Trek uniforms have always looked a little barren to me, and I thought that since these characters were supposed to be closer to Earth astronaughts than their successors it would have been nice to add some things.
3. Henry Archer designing The Warp 5 Engine
Instead of Henry Archer, I would have had it be Jonathan Archer who designed--or at least was lead designer of the engine. Part of the problem I had with the Archer character was that I felt he was fundamentally weak. Some of it may have been Bakula's portrayal, much of it had to do with awful writing, but conceptually I felt like Archer started out with a poor backstory.
Here is a grown man in his late forties whose biggest goal seems to be the preservation of the legacy of his father, a man we'd only seen once in a flashback, and cared nothing about. It's one thing in a story for a young man to do this--but given that Archer was supposed to be a pioneer and legend, it never seemed fitting that his rise was based on his daddy being someone important.
I felt the pilot would have been stronger if Starfleet had no confidence in the Warp 5 engine, they wanted to mothball the NX-01 and consider better Vulcan designs... but when the opportunity came to get the Klingon home and fast, Archer stepped up and said, "Let me show you what it can do. I'll take responsibility, give me the ship and I'll put together a crew."
Instead we got, "This is your father's engine." and, "Don't screw this up."
4. The Temporal Cold War
Even if every element of the story had been meticulously planned out and the ending determined and carefully laid out, it still would have been risky and fraught with plot holes. What made it a million times worse was that they had no idea what they were doing and made it up as they went along. It was a mess, just an awful mess that wasted so much of what could have been a great show. The whole time travel aspect of the show should have been axed before the start.
5. Getting out of the Backyard
The writer's bible that I looked at said that the Warp 5 engine would enable the ship to go beyond the 20 or so worlds and colonies that humanity had encountered so far to meet potentially hundreds of new species and civilizations.
Thinking about it, this was a flaw as well. Making the ship be able to traverse so far made it like every other Star Trek show. What it could and should have been was that the engine enabled humanity to move beyond the three worlds it knew, to about another dozen. The show could then have focused on building relationships with the Vulcans, Andorians, Orions, Klingons, Romulans and a handful of the aliens we know and love. They could have thrown in some of the TNG-era aliens here and there... but the main focus of the show should have been the forging of the Federation. Instead we got aliens of the week as usual, which was no different from Voyager. This also rendered two characters that th Writers bible created for their expertise completely useless.
6. Hoshi Sato
Had the setting remained within the confines of the "core Federation worlds" and "core enemies", Hoshi could have been instrumental in teaching Captain Archer and the rest of the crews the language, customs and anthropological background of the Worlds that were becoming important to Earth. She could have been the know-it-all that balanced T'Pol's know-it-all logic from a human side. She could have had relationships with Andorian, Vulcan and Tellarite warriors and diplomats that were different than Archer because of her awareness and understanding. Her role as mediator between them and Archer could have been incredibly dynamic. Instead, we got her pushing buttons on the universal translator saying "I'm doing the best I can!"
7. Travis Mayweather
Just like Sato, the second they left known space, all of his expertise on the Cargo industry, and all his knowledge of the local aliens and their treatment of space-faring civilians went out the window. 80% of his reason of existing on the ship vanished after the pilot. I can't possibly imagine why they would write that into the bible, knowing that it would be useless after the first episode. He could have been a foil for Sato... who as a scientist and linguist very much appreciated the aliens she came in contact with... he could have said "now hold on, they're not so great when they board and search your freighter for no reason whatsoever." Basically, when they explored strange new worlds, he knew as little as Archer did and thus could be no help whatsoever. By keeping the show in familiar territory, they could have utilized their intended purpose of Mayweather a lot more. At the same time, if ever they wanted to do an arc of episodes where they were in completely unknown space, such as what they did in Season 3, they could have used that as development for Sato and Mayweather "being out of their comfort zones", adjusting to new challenges and questioning their roles.
8. Armaments of the ship and crew.
I don't quite understand how the producers could say that the ship would have rudamentary technology and then introduce phasers, photon torpedoes and transporters ALL IN THE PILOT! They said, "you get to see it being developed, you get to see it in its early phases!" But the problem was... the phase pistols fired like phasers. The photonic torpoedoes fired like photon torpedoes. The transporter worked... just like the transporter. The differences were -completely- cosmetic, and there was nothing exciting about seeing it "introduced" whatsoever. We weren't even treated to a development and unveiling... all three were introduced in the pilot episode.
Now this may be BSG influenced... but visually they could have taken a different approach, with weapons that fired bullets, rail guns and nuclear weapons... maybe by season 3 or something, phasers would work their way in and other technologies as well. This could also have given Malcolm Reed more to do, actually tinkering with experimental technologies... seeing if these phasers he'd seen might put them on even ground with the aliens that were overpowering them.
9. T'Pol
They should have kept her as T'Pau and worked out a deal with royalties... but that was an understandable financial decision. The wig and costume for the first two seasons were awful. What were they thinking?! The third season look should have been it from the get-go.
A lot of T'Pol's development was ok. The decon chamber and Vulcan sensual massage were awful... but her marriage storyline and other things weren't bad. In many, many ways she was a stronger character than Archer, and the voice of reason. This is fine, but it also diminished the respect many of us felt for Archer. The Archer-T'Pol relationship was often balanced by having T'Pol be the injured damsel, and Archer saving her. This is ok occasionally, but I feel like it would have been better to give them an actual intellectual discourse, where some of Archer's motives and arguments were actually practical... rather than have him start intergalactic incidents because of his dog.
10. Dr. Phlox as a Denobulan
I loved him, and I thought the Denobulans were ok too, but they didn't have to introduce a never-before-seen race for a main character into a prequel. He could have been just as effective as a Tellarite.
11. Suliban
Same issue. They went the way of the Kazon anyway, but if they were always going to be special-effects hacks, why not just make them genetically modified Romulans, or even Remans? The Romulans could have been the villians from the get-go. The Romulan war was less than ten years away and we didn't see them until Season 4.
12. Timeline of the show.
If they assumed they had a full 7 years, why not set the show in 2154 instead of 2151? So that they wouldn't have to skip to 3 years in the future for the Founding of the Federation scene? They could have done 5 years of building the Alliances, with much of that devoted to solving the Andorian-Vulcan dispute, even perhaps having a Vulcan-Andorian War that Earth has to settle... and the final two years be the Romulan War and the Founding of the Federation. We'll never know of course what Manny Coto would have done with three more years if he'd had them, but really what cost the show dearly was the uninspiring and meandering first two seasons. If Season 4 would have been Season 1... we may have seen Enterprise on the air today.
1. The design of the ship
I didn't really mind it being a rehash of the Akira class, but never thought it was an original or marvelous design either. John Eaves had several sketches for the NX-01 that would have been superior final products. In the end the design alienated a lot of fans from the get-go, and hurt the show.
2. The Uniforms
A minor gripe, a deeper blue, less purple, I would have added name tags and a United Earth flag and Starfleet logo. Star Trek uniforms have always looked a little barren to me, and I thought that since these characters were supposed to be closer to Earth astronaughts than their successors it would have been nice to add some things.
3. Henry Archer designing The Warp 5 Engine
Instead of Henry Archer, I would have had it be Jonathan Archer who designed--or at least was lead designer of the engine. Part of the problem I had with the Archer character was that I felt he was fundamentally weak. Some of it may have been Bakula's portrayal, much of it had to do with awful writing, but conceptually I felt like Archer started out with a poor backstory.
Here is a grown man in his late forties whose biggest goal seems to be the preservation of the legacy of his father, a man we'd only seen once in a flashback, and cared nothing about. It's one thing in a story for a young man to do this--but given that Archer was supposed to be a pioneer and legend, it never seemed fitting that his rise was based on his daddy being someone important.
I felt the pilot would have been stronger if Starfleet had no confidence in the Warp 5 engine, they wanted to mothball the NX-01 and consider better Vulcan designs... but when the opportunity came to get the Klingon home and fast, Archer stepped up and said, "Let me show you what it can do. I'll take responsibility, give me the ship and I'll put together a crew."
Instead we got, "This is your father's engine." and, "Don't screw this up."
4. The Temporal Cold War
Even if every element of the story had been meticulously planned out and the ending determined and carefully laid out, it still would have been risky and fraught with plot holes. What made it a million times worse was that they had no idea what they were doing and made it up as they went along. It was a mess, just an awful mess that wasted so much of what could have been a great show. The whole time travel aspect of the show should have been axed before the start.
5. Getting out of the Backyard
The writer's bible that I looked at said that the Warp 5 engine would enable the ship to go beyond the 20 or so worlds and colonies that humanity had encountered so far to meet potentially hundreds of new species and civilizations.
Thinking about it, this was a flaw as well. Making the ship be able to traverse so far made it like every other Star Trek show. What it could and should have been was that the engine enabled humanity to move beyond the three worlds it knew, to about another dozen. The show could then have focused on building relationships with the Vulcans, Andorians, Orions, Klingons, Romulans and a handful of the aliens we know and love. They could have thrown in some of the TNG-era aliens here and there... but the main focus of the show should have been the forging of the Federation. Instead we got aliens of the week as usual, which was no different from Voyager. This also rendered two characters that th Writers bible created for their expertise completely useless.
6. Hoshi Sato
Had the setting remained within the confines of the "core Federation worlds" and "core enemies", Hoshi could have been instrumental in teaching Captain Archer and the rest of the crews the language, customs and anthropological background of the Worlds that were becoming important to Earth. She could have been the know-it-all that balanced T'Pol's know-it-all logic from a human side. She could have had relationships with Andorian, Vulcan and Tellarite warriors and diplomats that were different than Archer because of her awareness and understanding. Her role as mediator between them and Archer could have been incredibly dynamic. Instead, we got her pushing buttons on the universal translator saying "I'm doing the best I can!"
7. Travis Mayweather
Just like Sato, the second they left known space, all of his expertise on the Cargo industry, and all his knowledge of the local aliens and their treatment of space-faring civilians went out the window. 80% of his reason of existing on the ship vanished after the pilot. I can't possibly imagine why they would write that into the bible, knowing that it would be useless after the first episode. He could have been a foil for Sato... who as a scientist and linguist very much appreciated the aliens she came in contact with... he could have said "now hold on, they're not so great when they board and search your freighter for no reason whatsoever." Basically, when they explored strange new worlds, he knew as little as Archer did and thus could be no help whatsoever. By keeping the show in familiar territory, they could have utilized their intended purpose of Mayweather a lot more. At the same time, if ever they wanted to do an arc of episodes where they were in completely unknown space, such as what they did in Season 3, they could have used that as development for Sato and Mayweather "being out of their comfort zones", adjusting to new challenges and questioning their roles.
8. Armaments of the ship and crew.
I don't quite understand how the producers could say that the ship would have rudamentary technology and then introduce phasers, photon torpedoes and transporters ALL IN THE PILOT! They said, "you get to see it being developed, you get to see it in its early phases!" But the problem was... the phase pistols fired like phasers. The photonic torpoedoes fired like photon torpedoes. The transporter worked... just like the transporter. The differences were -completely- cosmetic, and there was nothing exciting about seeing it "introduced" whatsoever. We weren't even treated to a development and unveiling... all three were introduced in the pilot episode.
Now this may be BSG influenced... but visually they could have taken a different approach, with weapons that fired bullets, rail guns and nuclear weapons... maybe by season 3 or something, phasers would work their way in and other technologies as well. This could also have given Malcolm Reed more to do, actually tinkering with experimental technologies... seeing if these phasers he'd seen might put them on even ground with the aliens that were overpowering them.
9. T'Pol
They should have kept her as T'Pau and worked out a deal with royalties... but that was an understandable financial decision. The wig and costume for the first two seasons were awful. What were they thinking?! The third season look should have been it from the get-go.
A lot of T'Pol's development was ok. The decon chamber and Vulcan sensual massage were awful... but her marriage storyline and other things weren't bad. In many, many ways she was a stronger character than Archer, and the voice of reason. This is fine, but it also diminished the respect many of us felt for Archer. The Archer-T'Pol relationship was often balanced by having T'Pol be the injured damsel, and Archer saving her. This is ok occasionally, but I feel like it would have been better to give them an actual intellectual discourse, where some of Archer's motives and arguments were actually practical... rather than have him start intergalactic incidents because of his dog.
10. Dr. Phlox as a Denobulan
I loved him, and I thought the Denobulans were ok too, but they didn't have to introduce a never-before-seen race for a main character into a prequel. He could have been just as effective as a Tellarite.
11. Suliban
Same issue. They went the way of the Kazon anyway, but if they were always going to be special-effects hacks, why not just make them genetically modified Romulans, or even Remans? The Romulans could have been the villians from the get-go. The Romulan war was less than ten years away and we didn't see them until Season 4.
12. Timeline of the show.
If they assumed they had a full 7 years, why not set the show in 2154 instead of 2151? So that they wouldn't have to skip to 3 years in the future for the Founding of the Federation scene? They could have done 5 years of building the Alliances, with much of that devoted to solving the Andorian-Vulcan dispute, even perhaps having a Vulcan-Andorian War that Earth has to settle... and the final two years be the Romulan War and the Founding of the Federation. We'll never know of course what Manny Coto would have done with three more years if he'd had them, but really what cost the show dearly was the uninspiring and meandering first two seasons. If Season 4 would have been Season 1... we may have seen Enterprise on the air today.
I think they really looked like the link between contemporary space suits and the TOS uniforms. Also, they had pockets! Of course a Starfleet uniform would have to have pockets! 
