The idea that this game will turn into a counter pick fest because of variations doesn't hold any water. We have zero evidence that variations are of a "rock paper scissors" nature, where one variation will 7-3 this while another will get 3-7'd, based strictly on the zoner, rushdown, counterzoner archetypes, where zoner > rushdown, counterzoner > zoner, rushdown > counterzoner, etc, etc. It's not going to be like that. It's evident the base character determines alot, and while variations may alleviate problems, they may be more adjusting the sails on the ship rather than turning the tides of the ocean.
As for "this will reduce counterpicking"
This anticipation doesn't work. Assuming variations DO work as easy counterpicks for any situation- thus enabling even the fiercest character specialists to counter pick with a new variation- this will not allow someone who is losing to counter their way to victory. It doesn't work mathematically
My game theory formulation
Each players has 3 variations, one that goes 5-5 with everything, and two others, that go either 7-3 or 3-7 with the two other variations of the other player. Basically, each player can voluntarily make it 5-5, or they can counter, though counter leaves them open to be countered back the next round.
1) First round, both are blind pick, so both players will go for their most balanced variation, guaranteeing a 5-5 as to not risk a bad matchup. So long as at least one palyer doesn't defect, it is 5-5/
2) Player A defeats player B in the first round of a 5-5 matchup, therefore the most skilled player won.
3) Player B defects and counter picks because they lost, and chooses a proper counter
4) Player A is locked in place, unable to do anything about the counter
5) Player B defeats player A.
6) Player A is now able to counter-counter-pick while player B is locked in
7) Player A wins.
Even with variation locked on both sides, counter picking doesn't have any effectiveness so long as the ability to counter is equal on all sides. the player who is able to win 5-5 matchups will still overcome the player who can only win when the matchup is in their favor.
And all this is still ASSUMING the "rock paper scissors" counter picking scenario that everyone else is assuming from variations for some reason. I don't think it will even come to this. Injustice with its very diverse roster still has many characters that have a large abundance of 5-5 matchups. It's possible for characters to be very different without changing the odds of the match.