Runes are Unbalanced

That is, the fact they cost IP is unbalanced. It costs as much as a new champion to get a new page, which some people really can't prioritize. Altogether it takes around 13000 to add and fill a rune page. Which means that unless you either pay RP, or have literal days to do nothing but farm IP, you're stuck with what you've got. Which also means that you may be putting your team at a disadvantage if you attempt to play Ranked. You can't edit a page in the lobby, so you're fucked if you get stuck as support but only have your damage runes in place on both of the two you get to start.

They affect actual in-game stats. Why, then, do they cost points when Masteries do not?

Edit, some math for y'all: Okay. So let's say you win an hour-long game. That's 300 IP at the most. (Including WoTD bonus for an hour-long game) That's 21 hours of nothing but winning with 30-5 KDA, Every tower taken. And that's just to get the rune page. It's another 27 hours of nothing but winning with 30-5 KDA to fill it with runes.

That's a month and a half of play, if a person is to play a healthy amount, and gets the win of the day bonus. It's only a little less than that if you win every game and play two hour-long ones a day, because the second doesn't get the win of the day. Do you see the problem now?