I've also instantly thought "Thanks for that, PvP!". However, the cooldown is reduced to 20 seconds if you hit more than 3 targets.
So lets sum it up:
MSV:
Stone Guards: - Always full cooldown, except in LFR. Byebye Shockwave I think. But shouldn't be a big problem.
Feng (HC) - Shadow phase adds need more positioning now. This may suck. (have been @ Feng HC only once, don't blame me If I'm wrong :P). No need for a (Shockwave) stun in Normal mode.
Gara'jal: May have its full cooldown if you only hit 2 ghosts in the spirit world.
Spirit Kings: No need for a stun there.
Elegon: When meeting at the console for adds, there are always more than 3 targets.
Will of the Emperor: Should only have 40 seconds in the beginning, when two Rages spawn (10 man), but I wouldn't use Shockwave there.
HOF:
Vizier: No need for a stun.
Blade Lord: Same.
Garalon: Same.
Wind Lord: Blade Storm (+Bloodbath) is superior here IMO.
Amber Shaper: No need for a stun.
Shek'zeer: You'll have 3 or more targets when phase starts and that's when the stun is needed the most. Should be okay.
Terrace:
Protectors: No need for a stun here.
Tsulong: More than 3 adds after the big Sha-add dies, where the stun is needed most. I see no problems here.
Lei Shi: When you're tanking the elementals you also have more than 3, should be okay too.
Sha of Fear: No need for a stun here.
Challenge Mode
Okay I stopped running them after I got the Bronze title, so my memory may not be correct. But I think most add groups consist of more than 3 adds, so it should not cause big problems, however I got a feeling that some Gold tanks may get mad in certain situations.
Summary
Overall this change shouldn't be a big deal for us Prot Warriors.
But, in general, I wonder if/why Blizzard can't just change the whole spell and ability system once you are in RBG / Arena / BG.
Like "Spell Reflect PvE: 8 seconds CD (or how many it was @ BC) / Spell Reflect PvP: 25s CD".
Technical barrier or what?
PS: Don't care about open PvP