I hate Natures and the modern EV system. Outside of competitive (which I don't do
at all), they don't do anything but unnecessarily cut a Pokémon's potential and make catching and raising Pokémon more of a hassle than it's worth. There's nothing fun about resetting Legendary encounters 55 times so you don't end up with one with a crap Nature (Adamant Mewtwo, whoo-hoo!

), nor is catching 40 different versions of the same Pokémon or hatching 40 eggs of the same Pokémon. And, that's not even getting into the tedious, horrible grind that is EV training...
Abilities, I'm more mixed on. Many are really cool and useful, like Huge Power, Technician, No Guard, Speed Boost, and the weather abilities... And,
then, you have things like Poison Point, Static, and Effect Spore. In other words, Abilities that have no purpose other than making grinding even more tedious and sucking up your healing items (and thus, money). I would not shed a tear if these Abilities were permanently erased from the game.