For example, if we could SEE hidden values (which shouldn't be hidden, considering that dude in the Metro basically tells you what IVs your Pokemon has) and various other things. Basically, they could make it so the only things worth hacking are items or shininess. Those things do not affect gameplay (well, items do, but not in a major way) whereas things like RNG and GTS exploits and hacks do make it pointless to try and raise legit Pokemon and more or less ruin competitive play.
That, and the IV EV system as it stands now sucks.
Basically, make it possible to raise your Pokemon to be the best they could possibly be so that legit players have a chance to compete with hacks/RNGs.