Choice and Uniqueness
I'll keep this short, just an idea.
Some of you will remember the old talent tree for masteries and that alone made the game and give each champion a more unique way, your way to play plus the runes that those too you could customize how you'd like. Now the rune system now is ok but is a little limited and i get is for balance sake but a little customization for your champ would not hurt, to be like my Warwick is different from your Warwick not just in a rune system, maybe stats also... or the lazy way bring back the talent trees xD.