The major problem: Spirit Shell
Why is this a problem? It removes the ability of resto druids to be effective in most situations. I'm willing to wager the main issue with many healing classes being under average in HPS is due to Spirit Shell sniping the heals. If you want proof of this, look at any Vizier / Ta'yak log with a disc priest. It is comical.
Compounded, Spirit Shell is a 1 minute CD so it is up for almost every major damage phase that exists in MoP raiding. Re: Wind Lord Rain of Blades, Ta'yak Unseen Strike, etc. and it renders Parasitic Growth on Abmer-Shaper laughable with Divine Insight specced.
I love the spell, but in earnest, it is too powerful as it stands. It is causing balance issues.
Second contributor: Atonement
Atonement. We as disc identify with it, but how strong should it be? I perform on Ta'Yak as a pure atonement priest. That is I only case Smite, Holy Fire, and Penance on the boss, with the occasional shield, and the occasional friendly Penance/Cascade on the raid when in phase 2. Should I come remotely close to matching other healers output? No. Do I? Yes, and win by a large margin.
Atonement should be a trade-off. The utility of a class that can bring 35k DPS when actively DPSing as well as 35k HPS is such a strong argument that it is all you become. Atonement is also too strong for it's own good.
Last major issue: Mana pool, spell cost, and regen
The main problem with MoP is that the regen stat was clarified. Int no longer increased mana pool, which changed the way Disc regened, as well as modified other classes structure. The static mana pool, albeit a great move for overall enhanced play, caused an unforseen issue of balancing spell cost and regen. This is were I believe the majority of issues are falling. Druids are casting spells that cost too much relative to their regen, and it is causing them to fall short on encounters. It is this change that hasn't been properly adjusted for that has caused such a huge spread of healer output. It needs to be addressed.
How to fix it: Meet in the middle
The problem is right now if you nerf down Disc to meet the other specs, you are going to set back a lot of guilds in progression. The solution the resides in meeting in the middle. Drop SS and Atonement by a slight percentage. Buff druid healing slightly, as well as Holy Priest healing. In addition, re-balance spell costs. They don't seem accurate at the moment with the rate of mana consumption with the current healing specs.
I've said this about a dozen times these past few months, I prefer Holy Priest. But I won't put my raid in a bad position for my preference when the difference is so large.