The things that have always bothered me the most were:
1. We never saw what happened to Tom Riker
2. Kes was not a recurring character for the rest of Voyager, showing her changing into a Caretaker-like being. We just got that terrible episode Fury.
3. No Earth-Romulan war in Enterprise
4. No season 5-7 for Enterprise, or at least mini-series for Enterprise (see Earth-Romulan war)
5. No post-Nemesis movie with a mixed TNG/DS9/Voy cast...I would have loved to se that
6. No Nichelle Nichols Uhura in any of the spin off series
7. More of a complaint how Kirk was handled in Generations: his fate should have been more ambiguous, and he should have been pulled back into the Nexus somehow
8. I would have loved to see more of the post TUC-Pre-TNG era
I feel lately that Species 8472 should've been the "big bad" in Voyager's final season, and their "help", in a way, is what gets the crew home, instead of using the Borg again.
Yeah, I think 8472 should have been there somewhere in the finale. Maybe even as an ally to defeat the borg?
For a long time I used to I think the Caretaker (you know, the guy who brought Voyager there in the first place, or another of his species), should have been involved with the finale, somehow.
The Stargazer was allegedly supposed to be a Constitution class ship, so the story goes the actors even said Constitution while filming. But then higher-ups at Paramount overruled this and said they weren't going to allow a Constitution class ship on the show, resulting in the lines being re-dubbed to "Constellation class." Ironically, the model of the Constellation class ship in Picard's ready room since Farpoint was changed to a Constitution model for a few season 1 episodes, The Battle being one of them.
This.
But I agree, it would have been a lot cooler if the Stargazer was a Connie, and I thought it was a huge missed opportunity to have basically every class of ship to appear EXCEPT the Connie refit. We had Mirandas and Excelsiors and Klingon BOPs and K'Tingas somewhere in TNG/Ds9/Voy. Even had display models in the back ground of Connie refits and LCARS schematics in the first couple seasons of TNG. But alas, never the real thing.