I personally use Move Anything and just use Blizzards Runes. Move Anything lets you resize the frame as well and detach it from the character portrait. Then I use OmniCC to overlay the cooldown timers.
The Compactrunes author recently made some changes that bring it right in-line with what I wanted; vertically aligned runes with timers on only the actively refreshing rune, and refreshing from the top down. Pretty sweet. Its an excellent add-on. You will need to get the alpha version for now.
I have it located right below my character in the center of the screen, sized quite small, and set to only show in-combat. It properly allows click-through out of combat.