It's no where close to being a completely different character. Each variation shares strings and normals and walk speed and jump arc and even some universal specials. All variations does is adds two or three unique special moves or a slight altering of a few key strings. And yes, it does alter how a character functions but it's not as big of a jump to a whole new character.
And besides, even if variations makes things so different, who cares? So switching variation is the same as switching characters, it's not a big deal. Counter picking happens in fighting games, especially 2d fighters where characters have more defined roles. It's part if the game.
May I ask how are you certain of this when the game isn't even out yet?
Well b/c this is done at CHARACTER SELECT SCREEN.
This is changing character, thats it, no arguing about it. WTF, how can you deny the obvious.
Even if character shares 99% of moves with the other it is still different character as long as they're no identical in everything. If they all were named differently and looked differently there would be a shitstorm "WTF NRS trying to sell us army of clones" but "styles" are perfectly accepted and loved. Unbelievable.
As far as NRS games (as well as other FGs) go they are defined by special moves, it is not very hard to learn superman f23 or lanterns b13 or Kabals f23 etc, most chars have 1 or 2 usable stings its special that make them. Specials affect combos (you can already see it in Raiden reveal) so its not a matter of "not having to learn new combos" etc. Even though IMO anyone unable to learn character in NRS game should be considered mentally challenged b/c they are so easy.
In SF there are tons of similiar characters like Ruy, Evil Ruy or Akuma. Would be a good example of "variation". These characters although sharing 90% or moves still are played completely different b/c of "two or three unique specials"
The rest of your points already been adressed by me.