One of my biggest problems with it, is that the majority of user base don't want to play pokemon, they want to play smogonmon, I mean, overall, I like their rules, I may have some disagreements, but I can tolerate. I play in showdown without problems, in fact, I have fun on showdown.
But when I challenge one of my smogon adepts friend to a fight in the freaking console, he doesn't want to, because he can't make the fucking build that he readied on the smogon! In showdown he uses a m-tyranitar, a ferrothron, a smogonbird, and three random OU the team, but on the ds, he has nothing! He's clueless! He know how to EV spread in showdown by rolling some bars, but he can barely manage to SUPER TRAINING.
Oh god.
And the worst, I know that the majority of the "super competitive" players of smogon, don't know how to do it .
Many of then just pokegen and done, supah player.
Pokemon isn't just about battle, if you can't even turn your builds in reality, why the fuck you brag so much about it.
But aside this fact, meh, don't have many things to hate on smogon.