The holy/ret hybrid was nerfed at the start of Season 6, which fueled the migration to the deep prot build. With all the tankiness talents in the Protection tree, a prot healer would have a lot of stamina, a potentially everlasting Divine Plea, and most importantly Touched By the Light, which would rocket the paladin's spellpower above and beyond what he or she would have in a holy spec.
The trade off would be the loss of Holy Shock (no more instant heals), Illumination (but with an everlasting Divine Plea, who needs it?), Beacon of Light (which isn't that useful in 2s anyway), and other deep holy talents. But on the other hand, the prot healer gains a 20 second stun and a silence with Avenger's Shield. If one had a durable arena partner, say a DK or a warrior, then the instant heal might not be necessary, and the stuns and silences can lock up an opposing team's healer pretty well.
It's not hard to see why prot healing became popular for 2s. But it looks like it's going to end. Ghostcrawler wrote a couple things yesterday.
We are going to fix the specific scenario where a PvP paladin with a Prot build but spell power gear can heal for more than a Holy build in the same gear. We want to do this without messing up the Prot paladin trying to tank in PvE.
We will probably not make this change before the end of the current Arena season, but you can be thinking about your teams for season 7 with this change in mind.
Touched by the Light helps to solve a specific problem which is that paladins do both physical and magical damage and Prot paladins need both for threat (and damage). It works fine when the paladin is in tanking gear, and in fact was designed so that paladins wouldn't need to mix tanking gear with caster gear as they did in the past.
It is not balanced for a Prot paladin who decides to wear spell power gear. At that point you're double-dipping.
We have no problem with Prot paladins in PvP, but they need to be there because their survivability is an asset, not because they can out-heal an entire tree dedicated to healing.
There is a fine line between creative use of game mechanics and something that goes against our vision for the game. It's always going to be subjective. If the Retribution tree ended up being better at tanking than the Protection tree, or the Shadow priest was a better healer than the Disc tree, or the Marks hunter had a more powerful pet than the BM hunter, we'd take similar action.
While I'm sure the deep prot healers will not like this change unless holy gets some sort of buff to make up for it, I'm rather pleased with it from a design perspective. It just never made sense to have such a strong healer come out of the prot tree, to the point that being holy just isn't worth it for 2s.
My focus hasn't been on 2s at all this season, and I think some of that may have been because holy just isn't as strong in 2s versus 3s and 5s and I have to use this spec for PvE as well (or give up my tanking spec, which I don't want to do either).
While I do occasionally see prot healers in 3s, they're much rarer. It's more likely I'll see a Beacon of Light up signaling that they're deep holy, since a holy paladin has a much easier time dealing with split dps (Beacon one target, heal the other, and use Holy Shock for quick heals when the switch happens). When I'm playing 3s and 5s I generally Beacon one melee and then Sacred Shield our hunter (because everyone likes focusing the hunter). This lets me heal a melee while also covering our hunter.
In 2s there's not much split damage so Beacon's much less useful. Also, 2s focus a lot more on shutting down one player while burning the other, which a holy paladin is not very good at.
What I would like to see in Season 7 is a little more utility in a holy paladin. Shamans have their totems (which drop four at a time now!), Hex, and Wind Shock, druids have Cyclone, priests can Mana Burn and Psychic Scream. Paladins have a stun on a 40 second cooldown if they spec for it. Unless they're blood elves with Arcane Torrent, that's about it for CC and interrupts. We heal, and we bubble, but Hand of Protection only stops physical damage, making it of little use against DKs and ret paladins and just about everyone at range. Only warriors and rogues are really stopped by it, and a warrior can break it if he wants to.
I can't say I'll miss prot healing having never tried it, but I hope paladins in general get something to make up for it, especially for 2s. I'd like to give it another shot in Season 7.