It's really simple. The reason there isn't more cross breeding is because MK games are fundamentally different than Capcom games, and vice versa. So you won't see many top Capcom players dominating MK games, the same way you won't see many top MK players, dominating Capcom games.
The cop-out of "Oh, MK games are bad and don't take any skill... that's why the Capcom players don't do well in MK", isn't really valid. If the game took little skill, was easy or whatever, wouldn't these Capcom guys be easily dominating the competition with little effort? The fact is they aren't. Chris G is living proof that you can't just play the game at tournaments and expect to win. But the thing is, CHRIS G IS THE EXCEPTION! He's not someone I would call a Capcom player, since he's a top player in almost every fighting game he plays, same with Jwong. Yet these exceptions, they aren't winning. That's not to say MK players are better than Capcom players in general, but MK players sure as hell are better than Capcom players in MK games, to deny that is to dismiss the truth and live in denial. The exact same way that Capcom players are better at Capcom games than MK players are.