It would be foolish to ignore the biggest difference between MK and the rest of the major fighting games; it's American made. And because of that, it's built around entirely different sensibilities. That's not to say that ever Japanese fighting game is the same as the other, but you can see some nearly universal similarities between them that MK doesn't share. The easiest and most obvious example is blocking. In MK it has a dedicated button. In pretty much every (2D) Japanese fighting game (or at least all the ones that come to mind quickly), you just hold back.
Because Japanese games rule the FGC, they've become the standard. And because MK isn't one, it's not just different, it's wrong.
Soul Calibur and Virtua Fighter have block button too. That's not the reason. The reason is MK games weren't tournament viable until MK9. If NRS keeps making good quality games that people can embrace and go to tournaments for, in a few years MK will be just as respected as other fighting games.
The reason isn't Japanese versus American made either. It's all about the quality of the game. The fact of the matter is that, with the exception of MK1, MK2, and maybe Deadly Alliance, MK games before MK9 were simply not as well made as Japanese fighting games. So don't blame other games' fans for 'hating' MK, blame the former Midway for making crappy games, it's their fault and nobody else's. I mean, all you have to do is look back at MK Armageddon, i.e. the worst MK game of all time and literally the most broken game I have ever played, ever. Now, I am a die-hard MK fan, always have been. MK is my favorite game series of all time, but even I was disgusted with how awful of a game that was. So much so that I stopped playing MK and turned to Soul Calibur and Tekken. Was it may fault that I liked those two games and spoke badly of MK at the time? No, it was Midway's fault for making a terrible game.
MK vs. DC was also a bad game, let's just face it. I rented it, played it for 3 days, was very disappointed and, frankly, saddened, then I returned it and never played it again. It's the only MK game I didn't buy. I was playing Tekken 6 and Soul Calibur 4 at the time and both of those games were far and away superior to MK vs. DC, there was just no comparison.
Now, last year NRS finally made a good quality MK game and not only did a lot of old and new players flocked to it, I made a comeback as well. This is the most vibrant and populous MK community I have ever seen.
So what's the moral of the story? Don't blame Japenese companies (who, by the way, do make excellent games), don't blame other games' fans, and don't blame yourself. The blame falls squarely on the shoulders of the....MK team. Sad but true. It will take years and years of good quality games to erase the bad taste from the collective fighting game community's mouth. In other words, "if you build it, they will come".