I like it how TFF plays very much like a TOS episode, except with very large ambitions. The problem is that the film's budget apparently couldn't accomodate that vision. Otherwise, the film didn't do much wrong in my eyes. I still find the moments between Kirk, Spock and McCoy to be among the best and most heart-warming ever. The arrival at Sha Ka Ree is very true to the "where no man has gone before" premise of Star Trek, and it feels like discovering something awesome... much helped by the excellent score for this sequence. "God", I can't help myself, is chilling, especially when he takes Sybok's appearance. And I also need to praise Laurence Luckinbill's performance as Sybok here. In his last moments, you can see that he was not a madman, or a terrorist, just a believer, who gave up everything he had to find that which he believed would wait for him behind the Great Barrier. And now he realizes that te bad things he did were all for nothing, that he was duped. You can see shades of denial, shame, anger, sadness and simply heartbreak in his face as he confronts "God". Amazing performance.
There's a moment near the climax of the film when you really wonder if they were bold enough to say: Yes, in this film, our characters truly find God out in space. It would just fit with some of the things they did on the original show: Finding Abraham Lincoln (or something like him) in space, parallel Earths, or Alice in Wonderland. TOS never shied away from the outlandish and in the process managed to make space feel truly wondrous, a place where anything is possible. A reason for why I still find TOS to be the most exhilarating and exciting of the Trek series. But the resolution of it being a malevolent being that wants to be set free is also very TOS in its humanist statement that God is an idea that cannot be captured (and thus wouldn't need a starship!).... and an ideal as well. God is in the human heart, Kirk says. That agrees with TOS's stance on omnipotent beings as seen in Who Mourns For Adonais?, The Squire of Gothos and other episodes. The people of the 23rd century don't need a higher being to tell them what to do, because they know their purpose already. They don't need it as an explanation for the unknown, because they are intent on seeking out the unknown as a way of life, to understand it. Any being thus demanding to be worshipped acts out of selfish desire, not for the good of its "subjects". TFF confirms this again.
All of which leads me to hypothesize that you need to deeply love TOS, warts and all, in order to like TFF. Because if you do, you will be able to overlook the (mostly) horrible effects and the (sorry, Mr. Shatner) occasionally awkward directing job and might see that this story actually moves at a good clip, has lots of heart, and a grand, very Trekkian idea at its core.
The reason it got its bad reputation in 1989 is, I think, that, truth be told, it isn't quite as good as the other TOS movies - for reasons of production values, a rushed schedule, a director who overreached. But if you compare it to the TNG movies from today's perspective, one should go a little easier on it. Because those newer films showed us that you can do worse and, especially, less cinematic, less ambitious and less heartfelt Star Trek than TFF offered.