After The Killing Joke got ripped apart to make a different story for Batgirl I'm not sure the right people are making decisions at DC.
I hope I'm wrong though.
Whedon seems like an easy and obvious choice for this movie, although I'm worried it might be too obvious. He's got enough respect for Batman's world that I don't see him straying in the wrong direction. Looks like Whedon is also getting a bigger influence over the whole of the DCU, so we will see where that goes.
All in all, I think he can bring some freshness to the DCU and expect good things from him.