I think League of Legends would be better off without runes entirely.
Throughout League's history time and time again you'd see whichever champion could abuse the flavor of the month OP item rise to the top of the meta. You were playing the items, not the champions. Keystones do a very similar thing, you are playing the keystones and not the champions. This leaves champs who don't have a good keystone in the dust.
The best way to have a balanced champion pool is to just have champions. You can make specific changes instead of changes that effect a smorgasbord of champs, many irrelevant to the reason of change.
It would be nice if Riot considered toying with it now so they can get it ready for next season. :^)