Lowest shield comes first.

Usually it means "Illuminated Healing" from Hpal`s mastery =), then aegis/PWS, then big SS bubbles.
It all about numbers

lowest shields come first no matter what spellname or id it is.
If Shield A has 20000 and Shield B has 100000, then damage will be absorbed with Shield A then with Shield B.
I tested it like a month ago.

I think this point has been brought up to Blizzard many times since MoP launch, but they seem confident that the 30s cooldown is appropriate. I completely agree with them that a 0s cooldown would just result in us macroing the according chakras onto each and every spell, like hunters did with their aspect, but the current situation is not really better either.
Being subpar on one aspect and on par for the other (regarding single target and aoe healing) just because of chakras doesn't make for appealing gameplay in my book, it is just a hindrence.
The cataclym model also wasn't really good, but maybe a shorter cooldown, like you suggested, may be the solution to make holy more viable. But that would probably still not be enough, especially for 10 man, where you are not much in a fixed role, or even just for fast changing encounters, to bring it up to the level of disc. Even though disc will get changes/nerfs in 5.2, which I still can't understand to a certain extent, I think it is still in much better shape than holy, even with a shorter cooldown on chakra.

Maybe it is simply time to scrap the singletarget/aoe heal chakra and pack them together. I'd much rather have a choice between slightly buffed healing power overall (say everything 5 or 10% stronger) and a chastise like chakra for lulls during encounters and for the occasional questing/farming.
Its not like it would be a choice to use the heal chakra when healing, but it is also not a choice for hunters to stay in aspect of the hawk nowadays... they just are. Its more like an incentive to NOT be in the damage chakra.
Give the heal chakra hw: serenity, scrap hw: sanc, and still allow the rolling of renews, because that is one of the nicer mechanics of holy imo. The (slight) advantage in raw healing holy would have in respect to disc, and maybe other classes, through the buff from chakra would mostly be offset due to one of the worst masteries in a real raiding situation (druids and monks aren't that great either, but the other 3 are most certainly better than EoL).

I don't know if I'm missing something and just going nuts, or if this would legitimately be a good idea for holy, but it would most certainly solve the inflexibility that no other healer has to cope with. When they first announced chakras during cata beta I was pretty excited, but nowadays they are just a hassle

Moderator bump.