The powering up to 3, 6, 9, 12 are where the rewards is hidden, if you hit something good your body release dopamine and it makes you feel good, thus keep you addicted. I get it, the developer wants the runes to be like lottery tickets.
I farm all day, I only power up all purple with speed sub, but it still takes me hours every day to power up the runes, it's meaningless, and it's not fun at all. At this point, this rune power-up system is literally unplayable for end game players.