I think Star Trek IV is my favorite Star Trek film, although I have yet to watch VI in its entirety as an adult (I remember seeing it in theaters, though).
I appreciate the ecological themes and that it's another Star Trek movie about discovery, like the first one (my second choice).
I do also like the comedic milage we get out of them being confused and bewildered by 20th century Earth, and 20th century Earth being bewildered by them.
Actually, I think the next Star Trek movie should do an ecological theme like this. This movie proves that Star Trek can do it well, better than movies like The Happening or so many others.
Of course, what they'd probably do is remake this one and literally go with whales again, and it would suck. But I think you could do something in the spirit of this, be creative about it, and make a pretty good, relevant movie.
Oh, I also still need to watch the last two TNG movies. I was under the impression they are terrible but I need to watch for myself. TMP was supposed to be awful but I loved that.