The news that Joss Whedon is returning for The Avengers 2 (and will, in some way, be involved in the planned Marvel U TV show) is great. But it's even better than great, I believe. It's the cementing of Marvel Phase Two actually working.
By keeping Whedon an integral part of the Marvel CInematic Universe, Marvel Studios has essentially bought his support on their upcoming films. He's signed an exclusive deal with the studio through 2015, and during that time I can all but guarantee that he'll repeat the script doctoring he did on Captain America: The First Avenger. The original script for that film.... wasn't what you saw on screen. And word on the vine is that Captain America: The Winter Soldier could use some work as well. And that maybe Guardians of the Galaxy's script is far from fully baked.
What's more, his position as director of the next biggest movie in the world gives him weight to throw around at Marvel. I think the studio has been on a truly remarkable run - even counting the films of theirs I didn't like - but every run gotta end sometime. Bringing in Whedon as the central creative brain for Phase Two is exactly the sort of move that will keep the run running on.
What i'd love to see is Marvel start creating a larger braintrust, Pixar style. While they'd never really be able to have that Pixar feel - where everybody works in the same building - there's something to be said about creating a bullpen. Just like in the classic Marvel Comics days.
Thor: The Dark World might be too far gone for Whedon's saving touch (although who knows if he already did work on it), and Iron Man 3 is definitely its own thing. But I think we're looking at a pretty good run from the studio the next few years.