I can't speak to PvP so I will concede my lack on knowledge there, and in MoP on the PvE side I was Disc most of the time because I enjoyed atonement healing. That being said I was never told I couldn't come as a Holy Priest, I have however been told many times they wouldn't take another Disc Priest. I'll also concede that bringing up vanilla was silly, I wrote that post while drinking
Anyway low representation doesn't mean it was bad. It was because we were being compared to a healing that broke the game. Holy largely wasn't broken(At least for PvE), Disc was.
You are a Priest, you see other Priests healing for more and being pretty powerful. They can do things no other healer could and it wasn't particularly hard to learn to play it. Most people will make the switch to Disc after people on the sidewalk tell you its better. And from there most people don't want to have their duel spec as another healing spec so you don't play Holy at all.
In that past two years when I have been active on my Priest I haven't found an occasion where Holy was making me look terrible in the game. Most of my argument here came from you saying Holy isn't viable, which I disagree with.
I'm not saying disc vs Holy doesn't have a mountain of issues. But I bet if you have some gear right now you can log on, get in a raid group on normal/heroic and do just fine on the meters as a Holy Priest. If your concern is that their aren't enough, I think there will be more Holy in Legion when people decide they don't want to heal with atonement.
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I have a better example here, at least as far as your complaint on representation. Priest has always been cursed with the only class to have two healing specs. No other class does, no other class has two tank specs. So Holy and Disc are often unfairly judged against each other.
Now lots of classes have multiple damage specs, nothing new there. So what do you do when you decide you want to do damage and your going to PvE? You go online and you see what spec has the best damage. 12% play marks Hunter(Ty for the link). That is insane, when you compare Bm(0.7%), Surv(0.1%). That is even worse! Hunter is obviously the worst case scenario but still that is crazy. Hunters all level up and they see Marks is best so they all do it. More power to them, but the point is people do that with Priest to, and unless they make Holy and Disc not serve the same function that it will always be one or the other way out in front representation wise. People will always find the balance between easiest to play/best results. DPS rankings show Arcane well ahead of Frost Mages, but there are 30% more Frost Mages then Arcane(because Arcane is a bit of a bitch to maximize). So it isn't always even the best performing. And it just so happens Disc is kinda easy to be decent with.
This was a bit of a wall of text and I apologize, but Holy can heal in PvE. PvP I completely agree Holy is and has been in a bad spot(after so quick googling) this game has always been... iffy with PvP balance and I will leave it at that. But in a totally different topic I have very high hopes for their new pvp system in Legion so keep your fingers crossed!