I've played a lot of mobas and runes seem really weird.
I've played just about all the major mobas out there, so I like to think about how different games are balanced differently. And the idea of runes seems completely off to me. Riot has a couple of features that give new players a disadvantage, such as making the good champions prohibitively expensive, not allowing the jungle or other important summoner spells until higher levels, etc. But runes seem by far the worst. Who thought, "You know what this game needs? I bunch of out-of-match bonuses that cost a ton. That way new players can have an even harder time against veterans. Wait, what if we made it so that new players can't even buy the best ones? Great idea, write that down Jim."
Riot gives a lot of thought to balance, and they've admitted that runes completely backfired. But why don't they just remove the system entirely and refund people the cost they've sunk into it? That seems like a clean, relatively easy fix for a system that is completely against game balance.