I use PokeGen.
At the end of the day, Pokemon is game. The Pokemon you breed aren't real, the Pokemon I generate aren't real, and the Pokemon you breed aren't any more real then not real Pokemon I generate just because yours come from the actual game.
Using PokeGen is like using steroids. You don't magically gain muscle when you're on gear, you still have to train your ass off. Granted, not as much as someone who's natty, but you still have to train. I still have to make the make the Pokemon and get it to my game, just like you have to breed for selective things and then hatch the eggs. The end result is the same - Gains, or in this case, Pokemon battles. Yes, because I'm on gear I'll never be able to fully appreciate any of my victories, but I'm OK with that, because I'm still having fun, and again, Pokemon aren't real.