I'm perfectly fine with the current EVs, since all Pokemon can be EV-trained exactly the same. Natures also help to add more depth and variety, as you could have 3 stats that are perfect for boosting with a certain nature, and you're forced to decide what stat you want to emphasize more. That difference in emphasis could potentially make or break your chance of winning in battles. Also, all natures are equally obtainable by all Pokemon.
What I don't really, like, however, are IVs. I like how they add much more uniqueness & variety with Pokemon, but I hate it when bad-IV Pkmn (low numbered IVs or 0 IVs across the board) are pitted against good-IV Pkmn (31 IVs or pretty high IVs across the board).
Yeah, there's an extremely low chance of encountered 0-all or 31-all IVs Pokemon just like every other possible IV combo (I think 1 in 887,503,681) but generally, despite both Pkmn having good movesets and Trainers being educated in good Pkmn battling, a Pkmn with high IVs will always have the advantage over low IV Pkmn, no matter what (strictly in the IV sense, disregarding base stats since those are natural w/Pkmn anyway). While high IV Pkmn can attack with ease (based on pure power and high speed, tactics aren't needed if the foe can wipe you out with one blow first, even if you have Priority moves), low IV Pkmn need to be even more tactical, using Roar/Spikes, Sleep/Paralysis-inducing move+an decent attack, or drawing out battles to maximize Toxic's effect. And usually, pure power+high speed beats tactics anyday, since the foe can't even use their tactics due to an OHKO.
If there was a TM move that balanced IVs, that would possibly rectify the IV flaw. Not a noobie, over-powered, unbalanced move, just one that gave Pkmn with lower IVs a fighting chance. (the lower their IV, the higher chance that the user attacks first, and the lower their Atk/Sp. Atk IV, the more powerful the move). It would probably have ??? typing, so no Pkmn could resist it or be completely wiped out by it based on type-matchup. It would have a physical-special counterpart (like Hyperbeam/Giga Impact situation) to shift focus on Atk/Sp. Atk IVs. There could also be a version of the move for defensive situations, to utilize the Def/Sp. Def IVs. The IV total of a Pokemon could also be factored in some way, preventing 0 Atk-IV but-decent-in-other-stats Pkmn from utterly overpowering 31-Def IV but-decent-in-other-stats Pkmn.
Anyway, besides the semi-minor IV flaw, EVs, natures, abilities, base stats, typing, and movesets pretty much balance the game out, IMO.
*Sorry for going off-topic with IVs rather than EVs