What would you have done differently if you could go back and somehow influence some of the creative decisions?
TMP
This is the one I'd make the most changes to. The story has a lot of problems. The crew is WAY too passive, just sitting on the bridge and reacting to things for most of the story. And the big "revelation" about V'Ger at the end just isn't interesting enough to justify all the buildup. I'd ramp up the tension between Kirk & Decker (it just sort of fizzles out in the film), inject more of the action & humor of TOS, and have Kirk & co. take a more active role in the story. And I'd either reconceptualize & recast Ilia or just cut her altogether.
And I'd dress in the crew in something besides feetie pajamas. A two-toned version along the lines of Kirk's Admiral uniform could work.
TWOK
Not too many changes here. I'd try to plug some of the plot holes, like the
Reliant not noticing a missing planet in the Ceti Alpha system. I'd probably leave in the dialogue about Sulu becoming a captain, as that could be some cool foreshadowing for future films, and give him something to sacrifice in TSFS. And maybe boost the budget a bit.
TSFS
Most of my changes here would be with casting. First off, Kirstie Alley would repeat as Saavik, as I don't really care for Robin Curtis' portrayal.
Also, I feel that too many of the other characters are cast & directed to be idiots to make our heroes look good. Admiral Morrow needs to be older and have more gravitas (Honestly, I'd probably just bring in Brock Peters and introduce Admiral Cartwright a film early). "Mr. Adventure" is also too much of a stooge.
I'd like to see the Klingon bridge be something more like what we saw in ST:TMP and try to redress the TWOK torpedo room back to its original form. It'd also be nice if they kept the same Klingon bridge set for STIV.
TVH
I'd probably make the humor a bit less broad, as it doesn't hold up that great anymore. Alley as Saavik once again, and I'd probably have her accompany the crew back to the 20th Century.
I like Nicholas Meyer's idea of Gillian Taylor staying behind in the 20th Century to work to make sure that whales don't become extinct in the first place. I think that's better than the wish fulfillment of her following the crew back to the 23rd. It's a good message to send that utopia isn't going to just happen -- it's something we're all going to have to WORK for.
TFF
This is another one where I'd make a lot of changes. I agree with
Warped 9 that we'd need to get rid of most of the stupid broad comedy, as it just doesn't work here. The comedy in TVH arose naturally out of the situation the crew found themselves in, but here most of it is at the characters' expenses, and it just makes them look foolish.
I'd probably get rid off the majority of the "finding God" aspect of the story, and make Sybok more of a dangerous fanatic on an insane quest. I think this movie would work better as more of a straight action/suspense story. That'd be a nice break from the TVH formula.
I'd give the Klingons a rest for a film, as they've gotten pretty played out by this point. I'd also get rid of Sybok being Spock's long-lost brother and stick with Shatner's original idea of Kirk, Spock, and McCoy having a falling out of some kind. That could be fertile material to explore. And I'd give Shatner a boost to the budget so that it could have decent effects.
TUC
My main change here would be changing Valeris out for Saavik (played by Kirstie Alley again, natch). It would make her character betrayal a lot more shocking, and would tie off her arc nicely. It would also make the "a lie? / an error." exchanges make a lot more sense, as it would call back to TWOK. I certainly loved what Kim Cattrall did in the film, but bringing Alley back would've been even better.
It might be interesting to have the "gathering of the crew" scenes back in, especially if Bibi Beech came back as Carol Marcus.
GEN
Ugh... This one is pretty much a mess. I'd probably just eliminate the Kirk/Shatner stuff altogether, as it just doesn't work. A straight TNG story would be better.