He's halfway through a better-than-most Batman run and finished a critically acclaimed Superman run - why not let him have a crack at Wondy? Especially because, as far as I can tell, he's actually going to try and get into the better parts of the character - her FC role was about exploring the things he didn't like, such as the disturbed sexuality aspects; now, he's going to try and do for her what All-Star did for Supes. One particular quote I liked, in interview with Clive Barker:
Morrison distilled his mission statement into this: “To make it work, to give [Wonder Woman] a sexuality that isn’t exploitive, because that’s too easy; but also to give her a [narrative] power.”