Last comment: The way I see it is this -- people always constantly complain about their bad matchups in fighting games, but hopefully this is counteracted by the developer generally balancing the fighting game. So what this means is, the stronger characters hopefully don't have a ton of matchups that are very bad; but they also hopefully don't 8-2 75% of the cast.
Now, with a variation system, if the differences in playstyle between variations are significant, you might be introducing the option to *make* some matchups into bad matchups. Or to make matchups that might already be bad, worse. The conventional thought of "variations allow me to even up the matchup" doesn't apply if your opponent is constantly trying to pick the worst combinations for your character and variation, and vice versa.
Imo, constantly flipping a bad matchup in one direction or the other doesn't make for great gameplay or tournament experience. We've seen this a bit in Injustice with character roulette and it never seems to be a positive thing.. Half the time it doesn't even work out well for the people trying to do it -- but the other half the time the audience boos as we watch another week 3 Aquaman fight a snorefest of a match to knock a Catwoman out of pools.
The great majority of the most exciting matches happen when people stick to their guns, take a pause and a deep breath between games and figure out what happened, reassess, and then figure out how to play better. When they pull out every trick in the book, and dig deep into their character's options before giving up. So from a standpoint of encouraging the best possible gameplay, I'd side with encouraging the meta to be more about one player vs. another, rather than one pick vs. another (less HearthStone, more fundamentals).
If you can't get it done without trying to hard-counter both your opponent's character and his variation, focus on becoming a better player.. But trying to buy the right to double-counterpick players who are better, in the hopes of scrubbing out a win due to them being at supreme disadvantage, doesn't ring well and likely isn't very good for the tournament future of a game.