I like the runes as a concept, but this has been the problem that the overwhelming majority of the playerbase has been talking about for 3 straight seasons now... damage creep is out of hand.
Playerbase: "Damage creep is getting just a bit out of hand Riot"
Riot: "You're right, we hear you"
[A few patches later Riot nerfs lethality and makes most assassins---the class that should be doing damage---ineffective but turns Vayne into a complete assassin with the introduction of a new item (Duskblade)]
Playerbase: "Damage is still out of hand, except for the one class that should have burst actually doesn't, and the other class (mages) that should be able to have time to react and get off a couple of spells before they are instagibbed can't do that either... DAMAGE ACROSS THE BOARD IS TOO HIGH"
Riot: "Okay, okay... we got this... Hmmm... how can we fix this?"
[A season or so later]
Riot: "We've got it! You know how you guys hate the runes/mastery system?"
Playerbase: "Uh, I guess?"
Riot: "Well, check this out we're giving you a new mastery system!"
Playerbase: "Well... I guess that's okay, but..."
Riot: "Yeah, it's totally swell, keen, boss and all the other terms you kiddos are using nowadays to express happiness and enthusiasm!"
Playerbase: "Yeah... but... the dama..."
Riot: "We're gonna roll it out in preseason with a bunch of other changes that are really awesome that you didn't ask for, but make the game and your account so much more exciting!"
Playerbase: "Okay, but see there's still..."
Riot: "And we've given you even more ways to customize your playstyle!"
Playerbase: "Yeah, that's really nice, but there's still the issue of..."
Riot: "OH! And did we mention we added some runes that do EVEN MORE DAMAGE?!?!"
Playerbase: [facepalm]