Interesting thought experiment.
-I think improving the FX would definitely help.
-The novelization did a not-bad job of explaining things in the film that I thought could have benefitted from a bit more explanation, such as just how the E-A and the BoP manage to penetrate the Great Barrier.
-What I have a lot of doubt about is whether there's any way to make the ending more palatable to me. The whole "Looking for God" element inherently discomfits me, and what we get in TFF, besides obviously not being God in any meaningful capacity, is a huge disappointment. Kirk asks the obvious questions, and I feel as though a more interesting villain would have been better prepared for something like this to happen instead of immediately throwing any notion of omnibenevolence out the window. Angel may have even handled this better, as at one point Our Heroes in that series find an evidently omnibenevolent entity, and it's primarily through lucky accidents that they're able to overcome it.
-My secondary doubts concern the ease with which Sybok's goon squad takes over the E-A. It's never a good look for Our Heroes when they lose control of their own ship (see also "Rascals", "And the Children Shall Lead"), and it's even worse that apparently all it takes is a five second mind meld with most of them to make them become Shiny Happy People. The novelization at least gives this a bit more nuance, but there's only so much it can do. That even Spock and McCoy are initially swayed, and that it takes Kirk being Special to turn the tide, sticks in my craw. I would have liked to see Kirk's Inner Pain, especially since there are so many things we've already seen over the life of the franchise that might qualify, but mostly I would have liked to have seen Sybok's followers given some nuance and better motivation, and I would have liked to have seen at least some of the rest of the E-A crew trying to push back against Sybok's takeover.
-My tertiary concern is that the E-A being sent on this mission in the first place, as shown, makes no sense, but if the E-A had been fully functional and/or fully crewed than I don't see how the takeover would have been realistic to begin with. ...heck, in a way, there's very little about this movie that couldn't be rebranded and redone as a non-Star Trek film. (PIC could have done a season of his merry band going looking for Sha Ka Ree easily enough, and probably could have done it better.)
I guess you could say my feelings are that what we see on screen at times made me feel as though they weren't even trying, and that it's possible it could have at least been elevated to a "they really tried" state?