To be blunt, it's just a dumb idea. Why split the population in two for a moba? I don't see any advantage what so ever. The only reason I could see to ever have a similar system set up is a pvp based mmorpg.
Match making would improve, as players don't have to be on a specific side. It'll make it easier to group players based on language. Getting into challenges would probably be a lot quicker than not happening at all. I'm not sure who likes not having access to all the heroes.
Keep the faction system purely as a castle skin and ditch everything else that separates us.