This is a pretty good idea. What he's suggesting, is keep the way you currently gain EVs, but make it so that if you ever want to change your EV spread, or mess up a few points, or even want to use a pokemon that you've been playing with through the story, it's just a simple matter of choosing how you want your earned EVs allocated. Basically, once they're earned, you never have to lose or re-earn them.
Combine something like that with a way to alter natures, IVs, or abilities, and you'd have fully mutable pokemon, it may still take time to shift it into a new mold, but it would save you form grinding a new pokemon, and in the case of the extras I just mentioned, make breeding for the right combination of nature/IVs/ability less tedious.
Yup, you've got it. Im not entirely sure if IVs and Natures should be alterable, but Abilities I think could work. Just have every Pokemon have all of their abilities, but only one of them can be active at a time. Maybe their Hidden Ability is grayed out at first and has to be "unlocked" somehow (level requirement or something), and then can be selected after.
Maybe the new Amie system will serve to increase IVs? They did say they would be more visable, and they did say Amie would affect Pokemon in more ways than shown...one can only hope.
Unfortunately, I heard that it may instead increase critical hit rates and evasion rates. If that's true, I can't say I'm too happy with it, this game has far too much randomness as is and strategy suffers as a result. RPG mechanic or not, crits and evasion always leave a bad taste in my mouth, even in D&D, where they originated from. Win or lose, I don't want luck to be a factor.