Frequent readers probably realize that I play a priest as my main character. Most of my priesting life has been as discipline, but I've been playing a fair amount of holy since patch 4.3 dropped (I also flirted with it off and on in Wrath, but that experience isn't going to be relevant to this post) and the most iconic element of holy priest play (for the priest herself, anyway) is Chakra. This is the device around which the entire spec is supposed to, and does, turn.
Let's start with the good: Chakra was a great idea, conceptually. The idea of being able to fluidly shift from one "healing stance" to another, as needs and circumstances dictate, is a great idea and definitely was unique to the World of Warcraft healing game. It was to be the shining concept that, as Ghostcrawler put it, made people want to spec holy.
And, if it worked, it probably would have been successful in that goal.
The reason for this is that there exist, broadly, only two ways to balance a device like Chakra, which allows priests to choose between two* mutually exclusive stances: one that empowers raid, or area of effect (AoE) healing and one that empower single-target healing. These stances are Sanctuary and Serenity, respectively
*Forget Chastise stance, it's irrelevant in group PvE content
Option 1: You balance the priest such that when she is in Sanctuary Chakra, she is just as good at AoE healing as the other four (soon to be five) healing specs and when she is in Serenity Chakra, she is just as good at single-target healing as the other four/five healing specs. However, to make choosing a stance meaningful, the priest must be worse at the type of healing she is not in Chakra for, which creates the problem. In order to be just as good as any other healing spec at one type of healing, she must necessarily be worse than all the other healing specs at the other type of healing (it's not possible, nor even feasible even if it were possible, to shift Chakra states prior to each healing spell and it is not uncommon to need to sometimes cast some single-target healing spells while mostly AoE healing and vice versa). If the holy priest has 100% / 75% effectiveness (for the two types of healing) compared to the 100% / 100% effectiveness of all the other specs, the holy priest is clearly underpowered. She is significantly less flexible, for no added benefit over the other healing specs, who can do everything with no penalty.
Option 2: Let's solve that by giving holy priests a benefit. Let's make them stronger than every other healing spec in the type of healing they are in Chakra for, to balance out being weaker in the type of healing they are not in Chakra for. To put it simplistically (just to illustrate the concept, not be mathematically rigorous right here), if the holy priest is at 125% / 75% (for the two types of healing) effectiveness compared to the 100% / 100% effectiveness of all the other healing specs, that's balanced...mathematically. However, now the flexibility problem swings in the other direction. The holy priest is far too versatile. Any competitive raiding team will feel pressured to bring nothing but holy priests for their healing team, because a holy priest can always be the best at whatever the team needs at any given time.
You can craft a contrived, complicated system of healing involving Chakra that requires an immense skill cap, whereby an amazing holy priest can use Chakra to always be the best performer at the cost of having to work much harder than every other healing class. But, leaving aside whether that would even be fun, healers who are willing to work as hard will feel burned that they can't produce the same results with other classes.
Ultimately, this is very akin (though not identical) to the druid "bearcat" problem that Blizzard finally plans to resolve in Mists of Pandaria by splitting bear druids and cat druids into separate specs. Blizzard realized that it was a fundamentally impossible problem to solve when the two were differentiated only by a form change: either they had to gut one form, or they had to allow feral druids to be overpowered in terms of potential utility. While the specifics aren't identical, it similarly illustrates that you cannot allow a significant change in powers from something that can be switched in combat. It's impossible to find an acceptable state, where the class-spec that can shift its powers mid-combat is neither significantly underpowered nor significantly overpowered. It's not a matter of tuning numbers...the solutions lead to problems who's solutions lead back to the original problem.
To re-iterate, I think Chakra was a great idea, a very cool concept. If you could shift your healing powers while remaining in balance with everyone else, it would have absolutely been the shining reason to play holy. As it stands, it merely feels punitive...and the solution to that would be to punish every other healing class-spec in the game for not being a holy priest.
Sadly, it's time for a new device, a new centerpiece, for holy priests.