I really appreciate what MLG is doing for kof, but I feel that most people who go to tournaments don't really compete with an aim to win top prizes, but they are their to meet people and to have a good time in general.
When I go to a FGC major, I can go with a bunch of people from my area, even though none of them play kof, but that doesn't really matter, since we share a passion in fighting games. And when I get to the venue, I could meet many other like minded people and to meet up with kof players from other regions. And even though I don't really play marvel or sf4, I still enjoy watching their games and can join in with the hype since I have a general idea of what's going on in the games and who the top players are.
If I go to an MLG event, I will most likely have to travel alone, since none of my friends play kof, mk, or scv, so it will be a lot more expensive. And when I do get to the venue, most people there are either into real time strategy or fps games, so we kind of speak a different language. I can't really watch their matches, since I know nothing about their games and scenes.
Sure, I can seek out the 20 or so kof players, but I could do the same in a FGC major plus a few hundred players in other fighting games.
MLG needs to achieve a critical mass of entrants for fighting games, and it's a difficult job for them as long as they are running a few selected titles.