I think the trouble with Endgame was the trouble with Voyager generally, the writers weren't fans of the show...apart from Jeri Taylor, but she was so hung up on how awesome Janeway is that it stretched belief so much...Mosaic has her proving there was life on Mars - as a teenager(!)
The writers just treated Voyager as another writing job, which is fine as far as that goes, but when you're dealing with something that has an established mythology, and a show that has such a singular premise, then you need to be able to connect with the show or it's not going to succeed...
Say what you like about Star Trek (09), the writers went back and watched all the episodes of TOS and read a lot of tie-in literature in order to understand the show...when Ricardo Montalban agreed to do TWOK, he watched and rewatched Space Seed in order to nail his performance...
Start off with Voyager from the start, what's the premise?
We've got a ship in the Delta Quadrant - presumably for the rest of their lives, travelling home. So they have no allies, no hope of refuelling, no possibility of recrewing and a crew that, frankly, won't survive the trip...they have no medical staff, 30+ enemy combatants on the ship and several key officers dead...
Now, unless the writers actually care about this premise at all, then what is the point?
We see god knows how many crew members killed over the course of the show - and no one cares...even Enterprise was better in this regard!
We see way more than 40 torpedoes fired (and I know, I know people are already lining up to say "well they could just build more" which is fine, except that when the writers say "we only have 40 torpedoes, with no way to replace them, then we expect that to be true) When the Torpedoes ran out, why not have Voyager salvage disruptor cannons from an enemy ship they've destroyed and graft them onto the hull? Or build their own?
About 20 shuttles are lost...right...
Right - here's what I would have done differently...at the beginning I'd have had 3 bits of paper, and stuck them up in the writers room:
1 which read: "Crew Compliment"
1 which read: "Torpedos Remaining"
1 which read: "Shuttles Remaining"
And every time someone died, or a torpedo was fired, or a shuttle was lost I would have crossed out the previous number and updated it...then the show could maintain consistency with itself! Want to add crew to the ship in your story? Fine, do that and update the number, want a throwaway line that "The handling on this shuttle hasn't been right since we rebuilt it" fine update the number, want to trade for torpedoes? Fine update the number, but just maintain consistency! It's not hard!
There's a power shortage, except for the holodecks which have an independent power supply which is incompatible with the other ship systems (which is like saying electricity generated by nuclear power is different than electricity generated by solar power - ie bullshit) but this only matters when the plot demands it...
If they wanted to do TNG-lite, then they should have just done TNG-lite...they had a whole new Quadrant to populate, so naturally in the first season we have holodeck stories, a Romulan, a Cardassian, Klingon stuff...
I like Voyager, really I do, but the premise wasn't executed right at all - look at the ship in Season 1 and compare it to the ship in Season 7, really what changed? They got an Astrometrics Lab...and that's it...forget that they can't change the studio model, change the sets! Show them damaged and patched, show the crew making the ship looking more homely - plants, artwork etc have the crew start to pair off and have children, have weddings, have funerals, have birthdays not just to service the plot, but to show that there is life on Voyager - Janeway says to Ransom in Equinox "we've been known to let our hair down from time to time" When?
The writers could have done so much with this series...but they were - with exceptions - too cowardly and TPTB were too stuck in TNG thinking to allow any creativity...
I think Endgame was the epitome of this -
TNG's last episode involved the future uniforms - so Voyager's must
TNG's last episode involved the Captain in multiple timelines - so Voyager's must
TNG's last episode involved the Klingons as enemies - so Voyager's must
TNG's last episode involved the Captain making a mistake and using time travel to correct it
TNG's last episode involved a romantic subplot which caused tension/drama
TNG's last episode was awesome...damn it