PokéBase - Pokémon Q&A
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An EV trained Pokemon with IV and/or Nature flaws will be more powerful than a perfectly bred Pokemon (good nature and perfect IVs) provided the perfectly bred Pokemon has no EVs. I would recommend that you breed your Pokemon perfectly anyways, then EV train then, which will make your Pokemon crazy powerful.

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I forget their names, but there are certain Hoenn berries that reverse the process of EV training, so if you have a Pokemon that was bred well then you can reverse bad EV training with those berries and EV train them properly.