It's Clayface or it's Scarecrow are pretty good explanations, but unsatisfactory to me. Snyder has said again and again that this is his big Joker-story so it would be really lame to pull the old switcheroo on that.
Also, I know a lot of people don't like Snyder writing the Joker because he becomes a one-dimensional creep from a horror movie and loses all of the things that make him funny. I completely agree, but I don't mind because it works in his stories. However, I really hope that its not gonna be a trend in the New 52. As much as I love this Joker, it's not the one I want to keep seeing.
Then there is the 'Jim Gordon got out of Blackgate'. I honestly can't keep up with Batman Eternal and its links to the series and I just gave up and read them seperately. It saves me a lot of headaches.
All of that being said, I am really reaaaaally enjoying Endgame. The final page of the first issue got me really excited and there were quite a few moments in this last issue that did the same. Can't wait to see where it's all gonna lead!