As I've heard elsewhere, a big problem with the Academy is that it's basically filled mostly with old people who are unwilling to embrace new genres of film. That's why they'll usually go for the safe, conservative choices.
To them, superhero cinema has yet to evolve from the glory days of Adam West.
I mean, it took them god knows how many years to actually award a fantasy flick for best pic and they've yet to award a science fiction film. So maybe it should be no surprise that a superhero flick is yet to be nominated.