>>31183649That's what the training is for. Pokemon that are wild could get EVs appropriate to their level.
Levels 1-5 don't get any extra EVs so give newbies a running start but from level 6+ wild pokemon get some EVs. It could be done either as an overall gain like when you just randomly battle mons or the stats could be randomized so one wild one might be slightly faster or stronger than another.
This gives a good reason to breed: level 1 pokemon won't have EVs added so you can avoid having to retrain. It also gives some reason to catch and bother with low level wild mons.
As it's just training it could be undone and re-trained using whatever methods are in the game (ex: bags & berries) so mons found only late in the game won't be totally screwed up unless bred.
This will extend to legendaries/events/ect though at level 50+ in the wild so they will always have EVs trained keeping them difficult to catch.