This is just a theory I have so don't take this seriously. Stan Lee was the J.K. Rowling of his day with Spider-Man and everyone else his Harry Potterverse. His stories were meant for children. But because they had such a cutting edge and mature sensibility, adults not only really got into them but became the products biggest and most vocal fans. And that became the problem.
Slowly but surely comics started to cater to this very vocal fanbase and the industry began to take all of those little kids and young adults for granted. Because those adults didn't want what the kids wanted. The kids wanted escapist fun, free of overbearing complex adult issues. Or at least they wanted those things to be secondary. The adults wanted complexity, ambiguity, hipness, and relevancy.
Eventually they got what they wanted with Frank Miller and Alan Moore and every writer and artist who has followed in their footsteps or, at the very least, copied their approach to comics. Nowadays, most Marvel comics are just indistinguishable from The Watchmen and Born Again, stylistically anyway. Sure, there were some old schoolers who were able to balance the two approaches, like Chris Claremont and his team of X-Writers. But they've all kind of all fallen by the wayside nowadays it seems. The idea of trying to go back to what Lee and Kirby and all of their disciples were trying to do is met with scorn and ridicule. So Quesada is a symptom of what's wrong, rather then the source itself. The real villains are the fans who demand and cheer for this deconstructive, mature writing. All Quesada is doing is giving them what they want.
He does this because he knows all of those little kids and young adults and people who like light-hearted fun, who cried at the end of The Dark Phoenix Saga or cheered when Peter and Mary Jane got married, aren't there anymore to support the company. They're all watching Dragonball Z or reading Naruto mangas. They could care less about the adult-oriented Superhero genre of comic books that 20-30 something year old Internet Geeks love. Naruto and Inuyasha are escapist fun that cater to things they want to see and read about. Spider-man and The X-Men are confusing, overbearingly adult, and involve storylines that would be better suited for episodes of Deadwood or Nip/Tuck then Stan Lee's universe.
What I'm getting at here is that I think that the industry will become more irrelevant the more relevant it tries to be. They're kind of screwed at this point. If they try to go back to their children's stories roots even slightly, they risk pissing off their very vocal fanbase of people who think Joss Whedon is the greatest genre writer of all time. And it's kind of doubtful they would ever get those kids back, now that Japamation has it's claws in them. But if they keep doing what they are doing, they're going to become more and more niche. If anything, it proves that being relevant isn't always a good thing.
Again, this is just a theory.