EDIT ADDON: my thoughts on SFS failings, dumbnesses, wrong turns, all in no particular order ... I'm sure there are plenty of things I'm missing or going light on, but like I said, this last time I really enjoyed the movie all the way through, so I must be mellowing ...
Your ship is dead. The planet below is inhabited by armed klingons, and apparently is blowing itself up. There's a ship with only a couple people on it parked right next to you. Most of them are going to be dead when they come aboard your ship. So what do you do? beam to the other ship and take it over, then be in a position to rescue those down below, dictating terms to the surviving armed baddies down there? No, let's beam down to the exploding planet, then try to talk the reasonable-minded guy who just killed another starship and your son into bringing you up.
This is just one of several bits in SFS that are just recycling similar scenes in TWOK but giving them slightly different spins ... and it shows how you can reuse bits, but by doing so out of context, you're guaranteed to not achieve the same effect. 'You're going to have to come down here' in TWOK becomes, 'you're going to have to bring us up there to get it." Likewise, the RELIANT sneak attack scene plays out in SFS with the major deviation being Greedo -- sorry, the Enterprise shooting first. I think dramatically recycling the same bits with tiny spins is the dramatic equivalent to Meyer's take on tracking in pre-existing music to your film, that it is like getting kissed over the telephone. Diminished effect, to be sure.
The worst for me is the fact Kirk doesn't SEE his son killed. You can justify Kirk's reaction -- but to do so he needs to see it, not hear Saavik have to say the dramatically unplayable 'Admiral ... David is dead" line. You can justify a vidfeed from GoogleGenesis or from a klingon tricorder on the surface or however, but put it up there on the big viewscreen and let him see it happen. There are times when visual discretion is wonderful, but this is TREK's big SPACE OPERA film, with planets blowing up and sturm and drang ... the hero shouldn't be performing histrionics on the basis of what amouts to being a singing telegram.
As far as that goes, the interim between when the Enterprise automatics fail and when the self-destruct stuff happens ... shouldn't Scotty be doing his miracle worker thing for real right then, running down with Chekov and Sulu and trying to load a torp manually?
The whole 'backing out' of dock aspect was a really blown opportunity ... if you're going to do it that way, with the doors just BARELY opening in time, then Sulu should have had to rotate the whole ship through a quarter barrel roll to minimize the ship's profile while those doors were opening. A huge missed opportunity to do a real cliffhanging moment, instead of just playing at it and then cutting away to miss what should have looked like a similar moment in GALAXY QUEST and STARSHIP TROOPERS.
Spacedock - the idea of putting such a terrestrial-based concept in space is utterly STAR WARS, not Trek. Whether the spacedock interior really was just the deathstar2 reactor model or not (not inclined to going into that one again), it certainly LOOKS like it. More of the bigger-is-better bullshit, no notion of 'my what a big target I am' or how silly it is to put doors on a structure like this, just so they can fail. ILM started designing the TREK universe (even props!) with this one, and it was pretty much all wrong IMO. It's not just aesthetics either ... it takes you out of a movie if you see something that looks like it should be getting strafed by a star destroyer in a TREK movie ... or it should, anyway.
More trivial ones ...
The idea the ship is too old, when we're at most a decade or 12 years past the refit (don't bother quoting Okuda for the 'official' year, I don't buy that any more than the notion that the refit is a constitution -- it is ENTERPRISE-class.) More arbitrary plotting based on need to steer story a particular way without regard for legitimacy of notion.
The idea that Spock would stop aging because he was moved away from the genesis effect has from day 1 sounded as preposterous as anything else about Genesis. What, does that mean if Spock gets near green protomatter he'll suddenly start aging again? It just sounds like contrivance on top of contrivance, and arbitrary as hell.
Here's one I'll include apart from the others, because I don't know that it is dumb (it certainly works dramatically, and forms the basis for the remaining TOS pics in terms of making them seem very contemporary) ... the idea that Federation and Starfleet are so fucking paranoid about Genesis that they are throwing these guys under the bus and watching their every move and saying things like, "i don't think you ought to be discussing this subject in public." That's about what I'd expect from the US navy in 1967, when they told the crew of the LIBERTY that they couldn't discuss who it was that strafed them with machine gun fire and napalmed them and then torpedoed them after machine gunning all their lifeboats. The unevolved Federation from SFS onward in the TOS films -- even Nimbus III in TFF, because apparently that was designed to fail -- isn't just at odds with Roddernberry, but with a legitimate democracy in general. It isn't like section 31 is doing some black ops thing ... we're talking about spying on citizens and denying them freedom of expression. And it isn't even a specifically Starfleet thing, so it isn't like 'obey my order' ... the guy who takes McCoy in is FEDERATION security, not Starfleet.
All of that would be fine if they had kept Sowards' notion for TWOK ... that Starfleet had just abandoned the 'boldly go' policy in favor of just holding onto and protecting the systems they had, and that Kirk at 50 had his midlife crisis because everything his career was about was being discarded. So you'd have known this was a future that was reverting back more toward what we had ... and it would have been interesting if over the films the originally 'boldly go' got reinstated in part through the efforts and sacrifices of these guys. But that TWOK backstory didn't happen, which makes what follows seem arbitrary as all get-out to me.
My wife pointed out that some of the inexplicable reversals from TWOK to SFS (specifically Kirk going from 'I feel young' to "the death of spock is an open wound.") is kinda understandable given that grief is not a linear process ... you don't necessarily get better and better, you could have off days. So again, I'm being a little more forgiving.