Joss Whedon expresses his view about that missed opportunity:
"I'm as angry as you should be. … When I heard that I was like, 'I wonder ... no, I really can't do that. Oh, I already have a job.' I wouldn't clear the Avengers. I'm having so much fun with that sequel right now, just with the script, that I couldn't imagine not doing it."
Of course, like in "Star Wars: The Clone Wars", with cloning technology, a second Whedon could be manufactured in a fashion that he could direct both movies at the same time, but that's simply a little too science fictional.
The bright side to this is at least Marvel fans can rejoice at Whedon taking on "The Avengers 2" which will be released in the Summer of 2015, but on the dark side (no pun intended), fans can feel the force choking them out of being cheated of a Joss Whedon led movie project involving the rebellion and the empire. Though, if he did partake in "Star Wars", it might have some kind of "Firefly" feel to it. There is some kind of stunning similarity to Nathan Fillion's role that's a bit Han Solo-like. Both of them do "aim to misbehave".
The jury is still out on "Star Wars" having its director currently, but does have a release date.