"Well, one of the biggest problems with MK is just that he doesn't really have any even matchups or bad stages. He can't be counterpicked per se (with the possible exception of Diddy on FD, but I don't think Diddy can handle MK on many other stages).
Let me make a scenario for you to illustrate the biggest problem with MK so far. Lets say I use Mario in tournaments. Mario has a nearly unwinnable matchup against MK (or so I hear), so I need to use a secondary to take care of MK. But who do I pick up? Snake? No, MKs have learned how to beat all but the best Snakes out there. G&W? No, he still doesn't do great against MK. DDD, Falco, ROB? Nope, one of their worst matchups is MK right now. So I have to pick the one and only character that can handle MK: MK himself. Then I begin playing with MK so I can be good enough with him to make him my second... and I start to notice that I'm winning matches much more easily. I realize that no counterpick, be it a stage or a character, is bad for me because I can just switch to MK. I begin to rely on MK more and more whenever I feel pressured, so I start to pick him in the first game too, just to be safe. And that's when I discover that my MK, a character I only recently picked up, is better than my Mario in every possible situation. Soon I just stop playing Mario altogether because it is so much simpler and more effective to just play MK.
But lets assume there is no MK anymore, and Snake is the second best. Mario has a pretty tough matchup against Snake, so I have to pick up a secondary to beat him. Who do I pick up? Well, I have my choice from DDD, ROB, Falco, Pikachu, etc. There are quite a few characters I can choose from that do well, or even have an advantage against him (those characters above are actually hard counters). But each of those counterpick characters have their own inherent problems, bad matchups, and what not, so I can't really rely on them whenever I feel pressured against a character that goes even or has an advantage against them. In the end, I continue with Mario as my main and I use my second for Mario's difficult matchups but not much else. You know, what a second is supposed to be for.
Thats the biggest reason people are calling for MK's ban. In theory (and its actually happening currently), everyone will eventually switch to MK because they all need some sort of answer against him. And the worst part about this is that its like a virus. As soon as one good MK appears to tear up the competition in his region, a few people will realize that they need an answer to MK. So they pick up MK. Then because they pick up MK, more people need an answer to MK. So they pick up MK. Unfortunately, this isn't theorycraft or anything, since it has happened in several regions already and is becoming much more prevalent. Many high-level players have picked up MK in an effort to get him banned, and even tons of high-level MK players admit that MK should probably get banned. Of course, a big problem to this is the mindset people get into; matchups aren't set in stone, especially this early in the game, which is why I feel taking action now is much too soon. But one way or another, I can honestly see MK getting banned in a few months if a counter or two is not found soon."