I can see the Allies going this way, esp. if the war lasts a bit longer and/or is bloodier even than OTL. But the problem is, who's going to enforce it? Not many Germans are going to accept this situation - look at the very weak support for OTL's Rhenish seperatist movement - so the Allies are probably going to have keep forces stationed in the various countries for at least a decade to support the new governments against inevitable nationalist uprisings.
Also, if you're going to do this, you'll probably want to partition Prussia. Strip it of the Rhineland and the territories gained in the wars against Denmark, Austria-Hungary and France in order to set up a better balance of power between the new Germanies.
In the long run, the partition probably won't be viable, but who knows? After a couple generations people might get used to the status quo enough to kill the idea of a united Germany.