Runes And What Should Be Done With Them

Scrap 'em.

Riot just needs to admit they made a mistake, bring back the old Mastery system, but completely cut Runes from the game. Make people rely more heavily on their base stats, which would increase skill required, skill cap, and possibly even skill expression in more than a few champions.

Not to mention, without Runes, it would be a lot easier to tell which champion are truly OP and which are just taking advantage of strong items and/or the meta, thus making it easier for the inept balance team to balance champions.