No. The rune is never used blindly, so armor wouldn't effect it's use at all. We're only talking wakeup options here. Quan has no tools at all to deal with character's like Cage and Liu Kang. A wakeup EX Rune would be an awesome way to back them off when they keep rushing after a combo. But fine, not everyone has to agree. Most people seem to want armor on at least ONE move so they can escape rushdown pressure at the cost of a meter. And remember using meter for anything other than offense is a huge deal for Quan. I think an armored EX Skydop would be useless, since the move is still way too slow to hit them. It would have to be used strictly as an escape move. Seems like the only useful move to give armor to in a wakeup situation would be the rune.
But again, I'll trade all the EX Armor ideas for simply an unduckable punch at the end of the 1 1 2 string.