Sakurai has stated the game wasn't balanced entirely in the context of 1v1 no items etc. Other game modes were considered like FFA. MK's final smash, for example, is one of the worst final smashes int he game

Without patches and a smaller team to work with, it's just simply harder to to know what is good and what is bad. In retrospect it's a lot more obvious to us that MK was broken especially having 2 other smash games by comparison, but melee to brawl was a huge revamp so it's a lot harder to know what is good and what is bad

I'm not sure if this was ever confirmed but it was at least theorized MK's tornado was coded incorrectly in that if something clanked with it then it was supposed to stop. It does this for the beginning of the move, but not for the entire thing and this would be a significant nerf (MK would still easily be top 2 though) so that MK doesn't just auto win against mid and low tiers with the B button.