I think saying Spider-Man 2 is the best super hero movie is the same as saying that Spider-Man 2 is the worst super hero movie, except for all the other ones. Super-hero movie kind of stand on their own ground and can only be rated against each other, not actual movies; but I can always be proven wrong. Personally I think there are so many things that could have been improved about it, but in terms of plot and theme, it really captured everything that Spider-Man is about. He's not an adult, he's just a kid, he has no money, he has no job, he has no education, yet he's expected to always be there stopping crime. He never chose to do this: he has to.
It's interesting to see the movie explore how being Spider-Man is completely destroying his life and it's even more interesting to see him give it up, and afterwards, learn why he NEEDS to be Spider-Man, which is pretty cliche, but then again, what isn't? It's also about maturing and accepting who you are, rather than simply being a selfish asshole who wants to have everything and be someone you're not. The whole spiderman franchise is pretty much focused on puberty and coming of age, and when compared to other coming of age films, I also think this does very well.
I used to consider this the best super hero film I've seen, but I've reconsidered recently and this has moved down a spot.