I feel like, on top of all scaling issues, the rune system itself is obsolete and should be completely reworked in 6.0.
I think it should work like shadow orbs or soul shards and leave Runic Power to be the actual ressource.
For example, let's say a DK has one set of 3 runes: he could use them however he wants to increase his damage, his defense or use a special ability.
Then comes the Runic power:
Since hunters and rogues have a full bar of ressource available, Runic Power should stay the way it is and go the way of the warrior to be like Rage:
-Runic power generating abilities (auto attacks or cooldown-based small attacks)
-Runic power consuming abilities (heavy attacks)
This would help the devs to smooth out the skills, the rotation and the CDs of both DPS and tank DKs.
It would also prevent ressource overcapping for both RP and runes, for which we are currently the only class with that kind of issues. (warriors can dump rage easily, same for rogues, same for hunters)