The thing is PokeGen isn't perfect, not everyone can use PokeGen to create a Pokemon indistinguishable from a legitimately obtained one.
It's fine if you like to do that, but either keep the generated 'mons to yourself, or tell people you trade with that you used PokeGen to make them. Some people don't like receiving hacked or externally generated Pokemon.
I have used PokeGen myself, but only to look at how the game's underlying mechanics work, a person like myself who is quite skilled at technology can extrapolate a lot of functional information by looking at the interface of a cheating/hacking tool.
Personally, I don't care about IV's or EV's I just want to play the game legitimately and have fun. But people who obsessively breed for perfection or hack/use PokeGen make it impossible for me to even have a chance online.
I hope to battle you and have my 31 iv pokemon crush you. --- ANZ's most hated