I find TFF had a great underlying theme of the dangers of being a blind follower. Like TOS, it encorporated this theme without being too heavy handed.
It spotlighted the relationship of Kirk/Spock/McCoy better than any of the others, before or since.
Awesome character moments, such as Spock's birth, Bones euthanizing his father, Sybok's conversion of that character in the prologue.
The music was great.
Yes, I agree that it was far from perfect. The special effects, for example were clearly sub-par. (That's the nice way of saying it.) On the other hand, we can still watch TOS original special effects and not be turned off by it.
Biggest con: they pushed too hard to throw humor in, which turned out to be contrived, rather than evolving genuinly from the plot.
Personally, I think it was a terribly under-rated film.