TarkatanDentist
Kombatant
QFT (yes, the whole thing lol)But the thing is you can't switch variations mid match. You have to lose a tournament match in order to switch variations. So it is essentially the same exact thing as losing, and counter picking with a different character.
Just for hypothetical speaking, let's say Hellfire and Outlaw beats Grandmaster, and Ninjitsu loses to Grandmaster. If you pick Ninjitsu and your opponent picks Grandmaster in tournament, you wouldn't say Scorpion is at advantage. You wouldn't call it a 5-5 matchup just because the Scorpion has another variation that beats Grandmaster. The Ninjitsu is at disadvantage in that matchup. The Scorpion player would have to lose first, go down 0-1 in the set then counterpick with Hellfire. But literally there is no difference if he counterpicked with Outlaw instead of Hellfire.
Every variation is it's own character. You can't switch variations during a match. I could see your point if you could switch variations when you win a tournament match, but you can't. You can only switch if you lose, so there's no difference in counter picking with a different variation of just counter picking with a different character
I often think of variations as being roughly analogous to palette swap characters in MK games of old, in the sense that for most of them, normals usually stay mostly the same, but special moves become different. For all intents and purposes, different variations are different characters, straight up.
The tricky part is that the extent to which variations actually change the character's play style varies so, so much in this game. Reptile is a well-known example of a character whose variations scarcely affect his core gameplay at all, but then you have characters like Kung Jin where all three of his variations play totally differently, and then you have characters with one variation that's totally different, and two others which are broadly the same (Ferra/Torr and Kitana, with Lackey and Mournful respectively being the ones that shake things up), and more rarely other characters where the three variations are fairly similar, but with distinct advantages in differing match-ups (like Sonya).
Trying to make a tier list factoring all of that in is going to be one hell of a headache-inducer.