The inevitable conundrum, as has been pointed out already, is that there is no real way to gauge who should deserve seeding at the start of a new game. Most sports, when preparing to seed teams/players, do so with months of results on hand, or they have a method to measure seeds at the start of a season. Unfortunately, we're not playing the same game of Basketball this time around; it's a completely different game.
My initial gut reaction is to do it with a clean slate, and wait until there is some verifiable data to determine a seed. You often saw this in the Injustice era, where players would lose their minds on TO's for seeding and bracket issues that were taking into account many rounds of play (Pig, I'm looking at you). I'm not buying into the Shock/Summoning "Back in MY day" bull, but I really just don't think it's right to seed based on a previous entry in an unrelated series. Even if we were to do it by MK9 standards, why? That's ancient history by now, with many of the players considered super top have either faded from previous wins or simply not competed in a long time.
I can understand completely the need to make an exciting tournament by not having the big names eliminated early, or to have someone kind of float through, but at this point who can really determine what is a free bracket? We have no data. Can you make the argument as to what an easy bracket would be, based on prior game experience? Absolutely you could, and you might not be wrong, but again, there's no data to properly enhance that opinion. Otherwise, we cave in to the elitism that so many are accused of, and I simply don't think it's right at this point in time. Get some data, analyze that data, then make your decision.