Runes are unneeded and shouldn't be in the game
They hinder Masteries from being cool. They serve the same purpose as Masteries too. Removing Runes also make it easier to learn the game for a new player. So instead of learning both runes and Masteries; they just have to learn Runes. I think having Masteries be able to be something cool would be much better for the game and a good direction to take, and you don't have to grind IP for Runes and Rune Pages any longer, which was a pain for many players.
To address the people who have Runes and have bought Rune Pages with RP. You could give them a mystery skin for each one they bought with RP. Give IP Boosts for the runes (1 per rune owned?)
Now after Runes are gone you could make more Masteries and give out possible more Mastery points to build a nice diverse page depending on the Champion you are playing.