Something definitely needs to be done with rune combiner. Maybe there should be rune recipes?
Rune recipes would be interesting, but I don't know how useful it would be.
The question becomes what should be accomplished with lower tier runes?
Currently, lower level players unlock one rune slot per level AND they are limited to a certain tier of runes. In all honestly, one of those two systems should go. You then have a situation where if, by some querk in the system, a new player bought a few runes they like and they hit Level 10 and have to buy the upgraded versions of those runes, and buy the upgraded version of those again when they hit level 20.
It's this last point which the rune combiner pathetically tries to solve. I don't want to destroy 5 marginally useful runes for 1 random rune, I want to know what I'm going to get. Random runes should be a reward, not a punishment.
I know one thing that was mentioned by Riot the last time I saw them address this is that they don't want to dramatically re-do the rune system in a way that would cause people to feel jipped. AKA: Runes will likely retain their same price no matter what.