He's still a name director. Contrast that with, say, Singer, who has a much, much more successful television show than Whedon could ever have dreamed of having and a more successful feature film career and you see the difference. His failed Wonder Woman script notwithstanding, Whedon is in a position to control the story and the direction for any number of comic properties (Runaways comes to mind, in particular). The Avengers isn't one of them. It also doesn't speak to any of his pet issues (there are no gay characters and I don't remember any particularly empowered women in The Avengers, though that's not precisely in my wheelhouse when it comes to comics and I could be very wrong). I'm not saying I wouldn't be thrilled - I'm just saying, of all the things he could do, why would he do this? For that matter, why would the studio want him, given the trouble he's had hitting the mass market in the past? I don't think his movie (Cabin in the Woods) has even hit the market yet, has it?
Which, I guess, means that he couldn't write his own check. I guess I misspoke.