Yoshi mainers disagree about it being 55/45 for Yoshi. Snake is strongly debated, so while it may in fact be the case that's going to be a while before it can be determined, and since it's such a slim advantage if it does exist is hard to change how it works.
Basically, here's the problem with the advantage being so minor (And you did answer my question, I'm just explaining why it's not enough to make MK okay):
Round 1, Snake vs. MK. Neutral stage, 50:50.
Round 2, MK lost round 1 (Flipped a coin and he lost), counterpicks a bad stage for Snake: Better than 55:45.
Round 3, Snake picks his best anti-MK level: 55:45 Snake.
So just by playing MK, his absolute worst matchup at even skill levels gives the MK player better odds of winning. That's the best character that can oppose MK. Everyone else, just by playing MK, the MK player has shifted the odds of winning even though they are equally skilled even further towards his side because he can't be CP'ed to even 55:45 against him.
MK is a problem because at even skill levels, no matter what the opponent does, the MK player has an advantage that can't be overcome. Just by playing MK, he is statistically favored to win no matter what the response is, you can see it coming and you can't do a thing about it. No other character in the game can do this.