An idea I had recently, during a discussion about Flareon on another board - how about a set of hold items that swap two statistics - one each for each combination? So, for instance, you could have a Flareon hold the one that swaps Special Attack and Defense, so it'd have 95 base Defense instead of 60, and 60 base Special Attack instead of 95. It'd provide a way to fix some of the poor stat distributions without retconning anything, and it'd be entirely in the control of the players. You want to leave your Flareon with low Defense and increase its Speed instead? Just give it that hold item instead. Or you want to run it with Special attacks? Use one that swaps Attack for Defense or Speed (or whatever) instead.
It'd complicate prediction in competitive battling quite a bit - give a Cryogonal the one that swaps Special Defense and Defense, for instance, and that would certainly throw people off (at least momentarily), but aside from that, I don't think it would be an issue. It wouldn't be terribly unbalancing, in part because the stats wouldn't actually change - they'd just rearrange - so a low number would still exist, but would just be on a different stat, and in part because they'd be hold items, so holding one would mean that the pokemon couldn't hold anything else - lefties or life orb or a choice item or whatever.
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