OK, here is my hates after giving it much thought after reading through the other posts...
I will start by saying I am a child of the 80's I grew up with TNG onwards, and didnt like the original crew until Wrath of Kahn, so here goes...
TOS
I hate how starfleet is never shown in detail, just the odd official here and there with no consistancy.
I hate how every ship is either a cargo ship or a Constitution class vessal.
I hate how Kirk is always snogging the Aliens, its just pathetic and of its time.
I hate the miniskirts, how dimeaning to the female crew-members.
I hate how Sulu and Chekov were ancillery characters and they didn't have any personal relationships or life.
I hate the Klingons without the ridges, it feels very anti-black in its portrayal.
I hate the engine room being practically empty, and how all the rooms were disconnected from each other.
I hate the 60's look for everything, but this is as I look back at them, and cannot be justifyed at the time, but I will say I did and do like the retro look in Thunderbirds.
Phew thats that done, now onto the movies...
TOS Movies
I hate the bridge design for the Enterprise before Star Trek V. It actually felt less futuristic than the awful TOS bridge.
I hate TMP's pacing and premise, its dated badly compared to other films like Wrath of Kahn or The Undiscovered Country.
I hate the shoddy sets/locations used for the Genesis Planet in The Search for Spock.
I hate the captain of the Excelsior, not Sulu, but is it Harrison, and that Riding crop????
Ok, not so much to hate there
TNG
I hate the fact everyone wares such boring and skin tight/all in ones for their casual clothing.
I hate the fact that the Ships Councellor did not have any episodes with crew members undergoing intense sessions. So much lost potential in exploring deep psycological issues.
The Holodeck was such a crutch, and some of the scenarios were so contrived and felt out of place. God forbid a return to Picard as Robin Hood, or the Sherlock Holmes scenarios.
Not enough shown of the interpersonal relationships or families living on the ship. O'Brian and Keiko was as close as they ever got.
The Reset Switch...
The lighting of the set was so drab and boring. It doesn't have to be dark, but its just full brightness and no contrast. Generations made the Enterprise D look so much nicer.
I hate how every ambassador or admiral used an excelsior class starship.
The fact almost every planet was in a cave!
The fact that the Cardassian and Bajoran conflict was treated with such disinterest, its almost like ignoring the holocaust. Ro Laren was good, but how did she escape the work camps to join starfleet???
The first and only Clip Show!!!!!!!?!?!?! ARGH!!!
Most of this was new trek finding its feet...
Deep Space Nine
This is my newly favourite series. I never watched it when it was on air, but got them on DVD and fell in love, but as this is a hate thread.
The Changling infultration of the Alpha Quadrant was not really resolved, and much more of life on Earth and within the federation's politics could have been developed before the war started.
We should have had more of Dukat's inner demons, and his knowledge of the pah' wraiths could have been slower and more intreaguing.
Cardassians put on trial for their war crimes, and showing the bajoran process of recovery.
Voyager
Ok this was my favourite series before I discovered DS9, but it started badly and ended badly.
The conflict between the Marquis and Starfleet personel was resolved too easily.
The struggle to keep the ship going could have been an interesting way to create tensions and conflict on board.
The Holodeck locations were AWFUL, not a single one was good. Janeway as a childminder/house nanny, going to fairview and their WARPED view of Ireland, and then on to Da Vinchi?!??!
Neelix could have taken a bit longer to blend into the group.
Year of Hell should have been a 6-8 episode arc.
The Krenim could have been the best alien race from the delta quadrant, their whole attitude, the searches of the ship, Voyager could have become a ghetto like the jews in germany, smuggling people, groups of disperate races teaming together to evade them.
The void could have been an entire arc also, crew members loosing their mind, relationships breaking down. More of the captain isolating herself, etc.
The borg should only have come into play for the entirty of the final series. They are a great threat, but were cheapened with Species 8472, and Janeway's unbelievable ability to control them lol. We could have had crew-member thought dead for say 10 episodes, only to be found as still alive and then liberated, that way Seven of Nine (or actually known as the Horny Teen Magnet) could have either been ditched, or introduced earler as a borg drone Aparently disconnected, retracing her past (the raven etc) before becoming a threat in the final series.
Voyager should have ended with them coming home, and a final series, showing the crew go back to their normal lives, some successfully, some not, and Tuvok's mental instability becoming a feature.
What annoys me about Voyager is that it had some of the best episodes of any Trek, and had the potential of some great arcs, but was ruined by Berman, and the studios who passed at a year of hell season etc. This was along side DS9 which had the best characters and characterisations and the arcs with the profets/pah' wraiths, the changling threat, and the dominion war.
TNG Movies
Generations could have been better had it had started with the original crew and the Enterprise B, rescuing Guinen and Dr Soran. The old crew dealing with the death of Kirk, some in disbelief, and the hint he may have survived in the nexus. Then moving away from that era, and focusing on the battle with Soran and Picard, and Guinen warning of the Nexus.
Once Picard enters the nexus, he should actually be unable to resist the idea of staying in there, until Guinen introduces him to Kirk, and Kirk telling him his regrets and persuading him to go back for the crew, the ship, and for the future, and that be Kirk's final send off.
First Contact only has one flaw in my opinion, and that is the fact that Picards experience as locutus was not explored in as much depth as I would have liked. Flashbacks to the things he did, and things he experienced, would have helped sell his instability and anger. The borg experience is to Picard, what Kahn was to Kirk.
Insurrection this should not have been based around the baku and the sona, but could have been about Starfleet collaborating with another race to persecute and destroy another race. I know this isn't what Starfleet would usually do, but if it was a corrupt officer, and be a politically focused story, Picard could have become almost like the Marque, taking a stand against the Federation, bringing down the president himself, and causing lasting repurcutions for the future of the federation, which could have led into the next film, with the Romulans taking advantage of the situation.
Nemesis This is a controversial view, but I actually liked this movie. The thing I hated was the whole negotiations and potential of peace with the romulans became a backseat element. The romulans could be on the verge of civil war with the Remans, and their one great backup plan of infiltrating the federation, a clone of Captain Picard, is leading the remans. He could have started by destroying the romulan senate, luring the federation to the planet, before starting an all out assult on Earth. Then he comes face to face with Picard, and as he foils their plot on earth, Shinzon should have then become obsessed with Picard, and this would lead to the confrontation with the Prator and the Enterprise, and Data sacrificing himself to save Picard, without any B4 nonsense, this alongside the Troi and Riker Wedding, which we should have ended on, Happyness, and Sadness at Data's death, with Picard bittersweet ending the film on a slightly dark tone.
God that ended up longer than I thought it would, and to think all this hate is small compared to all I love about Star Trek!!!!