It sounds like he may be intending to stay more involved with shield than any of us expected, to the point of putting other projects on hold:
Originally Posted by Entertainment Weekly
EW: Will you follow up Avengers 2 with your version of Hamlet, which youíve been working on for 15 years? Iíve heard itís dark and controversial.
WHEDON: Thatís a giant endeavor, and Iím not planning any giant endeavors. I feel like some of the family stuff in [Hamlet] is even more twisted than we give it credit for. [My version] is no darker than any other vision, in certain respects. If everything works out according to plan, S.H.I.E.L.D. will be on when the movie is over and then Iíll already be too busy.
EW: S.H.I.E.L.D. is taking the Dr. Horrible sequel spotówhat would that have been like?
WHEDON: It would be [Dr. Horribleís] evolution, where he is now. What it was like for him on the bottom, what itís like for him on the top. We got a bunch of stuff written, and God knows the actors are willing. But I stupidly decided to make a TV show.