I could be completely wrong, and I probably should not have gone so far as to say the whole metagame, but if MK is out of the picture, Marth's worst match-up (and only truly disadvantageous one) is gone, which places him on the same pedestal as MK, that is, "He has no bad match-ups!" Jigglypuff, according to the Jigglypuff board, does not get destroyed by MK, while MK removes many other characters that Jigglypuff has a harder time with, such as Marth and I think Snake. Removing MK would harm Jigglypuff more than it has already been harmed. Yoshi's fight against MK has been a huge step forward in how people view him, albeit he's still negatively received for the mos tpart. Removing MK would pretty much knock off one of his big claims to fame.
Those type of changes would benefit some and hurt others, but really, if MK is not a character's worst fight, then removing MK, at best, won't affect them as much, but at worst it can really hurt them.