Them being separate allows the projects to try stuff the other group disagrees with and prove they are right. I very much like that.
Beyond that, the 2 projects really are VERY different. Again, with strict null and all the pain, it's causing on the TS side. It's not easy to just bring in features of one and merge them to the other. The entire architecture is different (eg: the flow inference). Then there's the pitty shit: I don't know if they're involved with TS, but some very visible Facebook people just can't handle the fact that the entire world doesn't revolve around Unix, as nice as it would be if it did.
Some stuff is sparking some collaboration. Babel getting support for TypeScript syntax for example.