Well I heard that if you have cheated Pokemon (PokeGen) it will corrupt your save file. I hope this is true. I have never played Pokemon on Wi-Fi because I know it's plagued with nothing but cheaters who generate their Pokemon. If it's true and there are only legit Pokemon online, you can bet your ass I'd be playing it daily.
I use PokeGen, but for respectable things. Today I used it to re-arrange the Pokemon in my PC, since it's faster that way. I've used it to re-name Pokemon instead of flying to the name changer's house and going through the dialogue. Since I have no one to trade with, I meet all other requirements for the trade evolutions then use PokeGen to evolve them. I had my Scyther and I made it hold a metal coat, then I used PokeGen to evolve it. I never use it to level up my Pokemon, alter their EV/IV, or anything like that.