Qui-Gon opened Anakin's eyes to the fact that he was gifted in The Force. That in addition to freeing him from slavery were the biggest turning points in Anakins life at that point in time. But the more important thing to keep in mind is that Qui-Gon is part of the recurring theme of loss.
Again, it's like a week they spent together. A busy, exciting week, but still just a week.
As for ST2, I viewed it as just a popcorn flick and was pretty happy with that. You can nitpick any scifi movie to pieces as to what was or wasn't realistic, and this has more flaws than it should, but overall a pretty fun ride IMO.
I do like your comment on Kirk's acension though. I think a lot of big budget movies get made these days with a sense of "this could be a flop" and because of that producers feel like they have to get to the peak of the character's existance ASAP. That bothers me. It could have been a lot more fun watchig Kirk climb the ladder a little slower, building his friendships and experience over time. Giving him the helm and every one of his crew (including Spock) becomming his instant BFF feels a little hollow to me.