Why would it be so hard to implement then? Just disable Dragon control for RTS, disable RTS control for player Dragon, send dragon player's input to RTS player's dragon actions, send RTS player's input to Dragon player's RTS actions, done!
Oh, it's just THAT SIMPLE, is it?
No offense, but you do not have any idea what you are talking about. Co-op multiplayer adds on a ton of additional challenges for how to communicate between the two players, there are player management issues, matchmaking services, and all kinds of other stuff that I don't know enough about development to think of.
Plus you have players who are are either saddled with an accidentally terrible friend, or saddled with someone who is DELIBERATELY griefing.
"Why would it be so hard"?!
There was a game that did something like this, and it had many of the same issues.
http://en.wikipedia.org/wiki/Savage:_The_Battle_for_Newerth
Larian, PLEASE, do not waste time and money trying to implement cooperative multiplayer in the game. I fear that you will discover too late that there are actually not that many people out there who are looking for that, and it will take valuable resources away from polishing and developing a more solid base game.