The two biggest problems with the reboot are Batman and Green Lantern titles, which weren't rebooted at all. But if DC had just waited a little bit, these problems would go away.
Geoff Johns' legendary Green Lantern run just finished, it should have been used as the finale for the Green Lantern franchise. Especially with all the epilogues for the characters - we know that despite being said that John Stewart will retire, Hal and Carol are getting married, these things won't happen because of the dinamic nature of comics books that unfortunately don't allow characters to have a real closure. But it could have been, if it was done before the reboot. And DC would be free to start things fresh with Green Lantern, just like they did with Superman and Wonder Woman.
The same goes for Batman Inc., which will end soon as well. Damian is dead anyway, so he could be retconned out for the New 52 without any real problem, and the timeline of Batman would be much less complicated. Dick would be Robin for the most part of the five year timelime and just recently graduated as Nightwing, Jason had a very small career anyway, and Tim would be the new Robin, a rookie.
Idea inspired by this site http://www.entertainmentfuse.com/comics/comic-features/damian-wayne-death-batman.html