The safest choice would be to keep the winner locked to both variation and character. With the ability to hidden variation select (which I believe has been confirmed, I'll have to check that later) it would become a silly guessing game of which variation the winner will select, negating the entire purpose of the lower being able to change character/variation.
Could you imagine choosing a zoning variation and losing to a counter zoning variation, then switching to a rush down variation of your character, only to have the opponent guess that you would do that and hidden select an anti rush down variation? It's pointless and could lead to a double counter pick against the LOSER.
I'll admit that we aren't fully sure how different each variation will be, and we could switch to a system of no variation lock at a later time. But let's go on the side of caution, and prevent the loser from potentially getting counter-picked. Once we run a few majors we will better understand the weight that variations have in MKX.
Edit: I didn't even bring up the stage selecting debacle at the beginning of IGAU. I don't think the argument of prior games apply, because stages, characters, variations, etc are different from game to game. We have to make the decision based on our game, and the goal of the developers.