A suggest for this would be "super" versions of the vitamins. Possibly to make a super vitamin you surrounded the original vitamin in diamond or something expensive of the sort. As long as the new method would be expensive it would be nice as you could avoid the grind. This would add the benefit of reintegrating mining into pixelmon at a more direct level. Especially late game.
PS an item to reset EV's to 0 (such as the reset bag (I think its called) would be useful so you wouldn't have to start from a newly bred mon of your favs.