Also, yes, other games have variations and remain totally locked, like SFA3, but the case with SFA3 is that an entire variation (X-Ism) is completely useless, and between the two remaining variations, depending on the character, one is definitely better than the other, with one specific variations (V-Ism) being better for a majority than the other (A-Ism). Variation freedom doesn't really matter here, because it would never see use anyway.
ST falls into a similar boat, where usually the 'New' character is generally better overall, with a couple exceptions (One character being defined by his 'Old' version, and a couple others having slight differences that do change matchups). It would literally only affect some characters.
These games aren't the best examples, because the rules work due to the lack of any reason to allow such a freedom. Also, with the two aformentioned games, the variations do not drastically alter the character's playstyle. Variations in MKX do. Old Honda will play pretty much the same as New Honda, just with slight, but effective differences to help in certain matchups.
For the vast majority, the freedom doesn't affect them anyway. Whereas for other games, it really does. We admittedly know nothing of MKX. HOWEVER, it's not difficult to see that, with how much changes within a character between the variations, that there are bound to be some really, really hard matchups along variations. Like 7-3s or worse. And characters may have a best variation for the scenario that may reduce this to just a 6-4 or even 5-5.
Yes, counterpicking has been in fighting games since the beginning, but games have done measures to reduce this beyond the simple balancing measures, and developers have even implemented options that are designed around the aspect of reducing the importance of the tactic.