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It destroys the game. I ask you, what is the point of playing a video game, if everything worth working towards in the first place, such as awesome pokes, unobtainable items, shinies, etc. is at your fingertips?
Unless of course, you just want to use it for Online Matchups. In which case, go for it. Although, I'd say PokeGTS is wayyyy better because it only takes like 20 mins of your time, as opposed to PokeGEN where you need to pay attention to like 50 settings for each pokemon..