Runes do way too much anyways, and if gotten rid of, there would be no more extra unexpected stats. Just flat "skill." No more airy teemo or dark harvest shaco. Champions would just be champions and do exactly as they do. Or riot could nerf it across the board. They affect gameplay way too much in my opinion.
I think that affecting gameplay a lot is the point of runes; to make it so that the game doesn't go stale, and so that Singed doesn't ONLY have to be played AP and so that Poppy doesn't always have to be a tank. It really introduces a lot of diversity and is great for people that just need a break from the meta stuff. If you take runes into account when you play, there's still a lot of skill expression going on (unless 
or 
is in the game).
