Batman fares well because he's been treated with a lot of respect lately in mass media. He's had 2 more than amazing films(changing the landscape of comic book adaptations) and an incredibly successful videogame, which also changed how superheros are handled in the industry.
Spider-Man on the other hand has had to deal with recent failures. Between a terrible final film and constant under performing video games. He has to build his rep back up with the mainstream. Bats had to do the same thing(Batman Forever and Batman and Robin).
I think Spidey will come roaring back though. He's too great a character not to. It just takes the amount of respect he deserves to get there which brings us back to the root of the problem. Activision. Unlike Warner Bros, Activision has no stake in Spider-Man, they don't care what gets put out under his name.
Nothing to argue about there. Only nitpick is that AA didn't really change anything, at least not anything that has been released or is about to be released. We still only got movie tie-ins and the occasional (Okay, more than occasional) Spider-Man game.