I gotta say, this thread actually changed my mind about this subject. I came in with the firm opinion that variations should be locked, just to keep things simple and consistent with the way they've worked in the past. However, the variation system itself is unlike anything we've seen in the past in MK, so maybe it's time to revisit the rules on character locks.
I am now firmly on the side of unlocked variations. This should reduce the effects of counter-picking, allowing player skill to have a greater impact on matches, without completely negating the strategy of counter-picking. It will also make the difference between some variations being viable or not. If variations are locked, then a variation with even just 1 or 2 heavily unfavorable matchups will likely not see much tournament life. But if allowed to switch to a variation that can handle those matchups, we should be able to see a much wider showing of variations and characters in the tournament scene.
As far as the benefits of a total-lock system, I really can't see any, other than putting more of an emphasis on the power of the character-select screen. But is that a good thing? My opinion is a solid "no".
TLDR: I think unlocked variations are healthy for the tournament scene and general MK community.