I'm not sure how you came to the conclusion that using single rune abilities would create set rotations with no variation. Between KM, Rime, Sudden Doom, AMS absorption and differing amounts of targets, your priorities would change. The fact that you would essentially have two rune resource pools actually makes things more interesting.
I understand that what I have laid out is a lot of change. And it may be difficult to perceive how it directly effects the way you play your DK. But, the design is solid. The gameplay would not be too different than what we have now. Things would just be more organized visually in a user-friendly way. But, by doing it in this specific manner, we open up new opportunity for better gameplay.