Well, I think that a wikia that has found a very effective way to deal with this kind of stuff is the Mortal Kombat Wikia. After the MK Reboot, they dealt with this by putting tabs in most of their pages. There's the Overview tab, Original Timeline tab, Alternative Timeline tab, Moveset tab, Fatality Theater tab and Gallery tab; obviously this is a bit excessive, I think only two tabs would be needed (Original DCU and DCnU). Since some of this characters are radically different, and adding more history to big pages like Superman's would make them way to big, I think this is a pretty good way to deal with this whole DCnU thing.