Earlier quoted context omitted.
To be fair, this pretty much ends after you have basic rune pages and hit level 30. I mean, ok, maybe you don't have the perfect runes because mana runes were good on Ryze (and terrible on every other champ) or something, but even with max rune pages, you can't really account for every champ very well (and believe me, I've tried, as I ARAM with everyone...)
That's still a decent time investment, also in league you don't even have access to all the heroes without a huge time/money investment, everything other than player skill is even in dota.
They've talked about reworking runes, but I take it they don't have any good ideas about how to fix things. As you say, many players have a lot of time invested in them. I mean, I'm personally down to only needing crit damage and mana runes, so that should tell you something.