I figured out why they did the runes thing, it's still a huge mistake but I understand why, now.

They were planning on doing massive balance changes/reworks anyways, and decided that since the old rune system had such a massive depth of stats, that the old system would amount to "herding cats", that is, given the sheer amount of capacity the old system had, no matter what balances they made there was simply too much stats to balance everything. I'm pretty sure the idea here is to consolidate runes and masteries so they can do those balance changes in a framework that can actually happen.

I get it, it's just sad we have to suffer while they fix it.