It's possible that the pokemon could become a dominant member of its species, perhaps. If, say, a level 90 rapidash with unsual moves was released into an area where other herds of rapidash resided, it might bully other members and establish its own place. If it's female, it might settle more peacefully, but if it's male, it may well fight several stallions for their herds and, being stronger than most (or all) wild stallions, it could control a much larger herd.
That is, of course, if the animal hasn't been neutered.
It probably wouldn't upset the balance of nature very much at all, but it might have a fair impact on the genes of the next generation, if it had the ability to breed, I guess.