I'd really like a way to integrate EV training into the main game without it being intrusive. Super training and Hordes were nice, but still a tedious detour that interrupted your journey which either ended in you becoming overlevelled or wasting hours punting soccerballs.

Add an NPC you can speak to named Mr. Focus (or similar), who can teach your pokemon to 'focus' their training on certain stats - meaning that they only receive EVs when they defeat a Pokemon that yields that kind.
Make the game's trainers have good EVs too, to compensate for the increase in power you now have.