Two QBs in the game is an interesting idea, but it's got some serious weaknesses to overcome:
1) It's extra vulnerable to a blitz, because your QB without the ball is probably not going to do as well as a RB/FB at blitz pickup.
2) You'll need two QBs capable of both running and passing, or you won't get any advantage from the misdirection.
3) If you split your blocking scheme, half for each QB, it's a lot easier to get to each. If you don't, the defense can just read your blocking to know where the ball is going, maybe leaving one guy to defend the QB without a pocket.
4) If the QB receiving the snap isn't running out for a pass, you've lost an eligible receiver. It's much easier to defend 4 than it is 5.