
I admit I haven't read back through this thread yet, but here are some off the cuff reactions:
I do still sort of question the idea that an action-packed, Kirk-heavy story is truly "old fashioned 'Star Trek.'" And, as I've said, I think ST V is a lot more than that, and is not obnoxiously all about action, all about Kirk. I would like to think the character moments for the other characters were not forced on Shatner. I think it speaks better of him as an actor and a thinker if he planned a story that really isn't "all about Kirk," because this movie really and truly is not.
"No Star Trek without Kirk's ego" -- ? Just sayin', who got more fan mail back in the day, Nimoy or Shatner? I don't think arguments like this are ultimately that productive, though. It really took both of them, along with De Kelley (although I think to a lesser extent). I'm glad we got the characters we did in the proportions that we did.
You're darn right I'm a Sybok booster, and I always will be. Such an intriguing idea, and so well played by Luckinbill. (Now, thank goodness they didn't get Sean Connery as was the original intent -- I think that really would have pulled folks right out of the film.)
You should read the novelization to learn more about J'Onn, Sybok's lackey (like Scott said). J.M. Dillard gave him quite a good backstory. Likewise for St. John Talbot. Caitlin Dar, too -- turns out she has a Welsh (Irish?) ancestor a few generations back, hence her wacky name (Scott asked about this on the forums a few weeks ago).
That's not a Voyager probe, Scott. That's Pioneer 10. See: http://en.wikipedia.org/wiki/Pioneer_10.
Another nice thing Dillard does throughout her novelization is deal with the various characters' relationships to the 1701-A vs. the 1701. I had never really thought about it, but things like the "tall ship" scene don't really work in the same movie as "I miss my old chair" unless you do some character work, and Dillard, to her credit, does it and does it well.
I remember being SO furious when Goldsmith's TMP theme was used for STV *after* being co-opted for TNG! Especially since ST V basically starts with a "teaser" before the opening credits. I thought, "Why are they making this structured like a 'Next Gen' episode!" Ha. It doesn't bother me now and, as you said, Goldsmith's score really is a great one.
I really like the nautical-themed observation lounge, too -- but might it, and not the Nimbus III saloon, be the redress of Ten Forward? At the very least, doesn't it use the doors with the Starfleet delta etched into the glass, just as the President's office will in ST VI? I could be wrong, I haven't gotten around to rewatching it again yet.
Ooh, I really like Chris' interpretation of the chiaroscuro camera work!
Again, Dillard's novelization goes into great depth about what Spock does and doesn't choose and why, and it is believable. I can appreciate Scott wanting more in the film itself, but, remember: Vulcans are INTENSELY private people -- and Chris raises the excellent point of Sybok's rejoinder: "You didn't know this about your friends?" One could even make a case that the film argues that friendship is not about knowing everyone's deepest, darkest secrets -- rather, it is about accepting them when and if those secrets come to light, all the same. It's a form of love, and, as the Bible says, "no one has ever seen God; but if we love each other, God's love is made perfect in us" (1 John 4). Appropriate for a Trek film whose ultimate judgment on the God question is, "Maybe God's not out there, but in here -- the human heart." I think it works.
No one ever says "You're a Romulan!" because, by this point, TNG has established that Romulans have not only pointed ears but also ridiculously large shoulder pads.

Dillard even manages to redeem the Uhura bit, although right now I forget how.
You mocked the Sybok-Spock reunion scene, but that's one of my favorite bits in the whole movie. Luckinbill is so engaging, and Spock's response -- the halting way he says, "Yes... you have committed 17 violations of Neutral Zone treaty" -- awesome stuff! How can you be hating on that?
Now, here's something I've never been able to understand: how is Spock free to go and get his anti-gravity boots? Does no one stop him and say, "Hey, where do you think you're going?" Has never made a lick of sense to me. (Even Dillard can't explain it in her novel -- it just happens.)
Did you notice that they go past deck 78 2 or 3 times, too? Ugh.
He's probably calling "anyone in the sound of my voice" so as to get help ASAP.
What would it matter if Spock was naturally conceived or not? He still could have been carried to term in Amanda's womb, even if he was conceived in a lab. Doesn't this happen all the time today in IVF treatments?
For what it's worth, Kirk's unseen pain in the novelization is regrets over Carol and David, although I like all of your suggestions, too. (Although if they're not going to bother mentioning his brother George, then there was no way they were going to dredge up Edith Keeler or Miramanee again, had Kirk submitted to Sybok's "treatment").
The barrier in "Where No Man..." is at the edge of the galaxy, not the center. So they couldn't have been the same barrier. Maybe they could have made the Great Barrier look like the "Galatic Barrier," but not the same one. (Again, Dillard does a far better job of this than the movie does -- it's just intense radiation, etc., metaphorically called a "barrier," and Sybok's scientific training comes to bear as he helps Scotty reconfigure the Enterprise's shields to withstand the radiation, thus explaining their relatively easy passage.)
Wasn't Doc Brown's dog Einstein, not Copernicus?
I don't understand "chasing God" to be the problem because, of course, as Spock says, "This is not the God of Sha Ka Ree, nor any other God." I just must not be following your objections to the plot. Are you saying they *should* have found God, or maybe definitively disproved God, or something? Ellison's pitch, at least as you've summarized it, is totally off the "Star Trek" path. One of Trek's great themes is that there are huge mysteries and wonders in the Universe, *and* we can wrap our minds around them. Think about the resolution to the TNG finale. Kirk is doing what he always does: taking down false idols, just on a big scale. I think it's a great ending, and really the only one possible.
(Your criticism of it being too much like Armus, ok, that I get. But the rest I just didn't follow -- sorry.)
Dang, you guys are tough on the end of the film. Especially when you've already said you appreciate it for how it explores the friendship between the Big Three. I am really surprised how harsh you guys were when it came right down to it. Go figure.
Fun commentary - thanks!