I think Joss Whedon fell victim to the "company line" over at Marvel.He's been throwing a lot of subliminal(some blatant) shots at Marvel lately.
He even said he was forced by Kevin Feige to kill off agent Coulson in the first Avengers.
He's always had that weird, frustrated homosexual vibe, but I think Marvel put the puppet strings on him.
It's funny that Age Of Ultron is his final film with Marvel and one of the main themes of the movie(mostly during promotion) was "Now I'm free...no strings on me"
I remember how he praised Edgar Wright's Ant Man script after Marvel gave Edgar the boot.
Seems like creative people have a hard time sustaining any kind of relationship with Marvel