Imagine a game with three DPS classes (Ignore tanking and healing for now.) Our first DPS class, "Mcweaksauce" can pull 4,000 DPS. Our second "Balanced" can deal 5,000 DPS, and our last, "Imba" can deal 6,000 DPS. It'll take some time to gear up to these levels, so we'll assume players are doing slightly less DPS in the beginning. If we assume a raid has 25 players, of which 3 are tanks and 7 are healers, we have 15 DPS. What should the assumed damage of a raid be?
Most guilds will have a mix of all classes. Assuming a reasonable distribution, we could balance the raid around have 15 Balanced players, for a total of 75,000 DPS. If you're below 75k raid DPS, you're in trouble, either brushing up against enrage timers or getting two waves of adds on fights like Sartharion, or two teleports on Noth (lol?)
Then, we can set up progression. Fights 1, 2, and 3 only take 60K raid DPS. Fights 4-6 take 70k, and fights 7-10 take the full 75k. This means people can gear up on the initial fights, and only later manage the difficult ones. But, we have a problem. While an AVERAGE raid might have to take time progressing through easy content, a raid full of Imbas might be able to clear the whole place while undergeared. And god help any guild with too many Mcweaksauces, they'll never make it past the first sector, even with gear.
This exact problem happened early in Wrath. A few classes, primarily BM Hunters and DW Death Knights, and Sub Rogues were doing so much DPS that stacking them gave a raid a huge advantage. Some of this was due to bugs, some were mere oversights where DPS issues hadn't emerged on the PTR. The result, however, was relatively devastating; Encounters that should have been extremely difficult were instead trivialized. "Gearing up" didn't exist at all. By the time bugs and absurd-DPS issues were resolved, people had enough gear that the real versions still weren't difficult.
I'm going to go out on a limb and say that Blizzard can never, ever balance all classes completely. There will always be some unpredictable side effect of a talent combination or gear setup that causes some class to be stackable for extreme damage. That issue is something that basically has to be taken in stride and reacted to rather than prevented. However, there's another issue that's entirely predictable that has the same symptoms.
Consider a class called Supercooldowns. This bad boy can pump out 5,000 DPS. But there's a catch. Every 30 minutes he can use an ability called Spinach that triples his damage for a full minute. If a fight lasts 5 minutes he will normally do 1.5 million damage. However, every 3rd or 4th attempt, his cooldown will be up. He'll do a blistering 2.1m damage, 40% more than normal. Now assume every class is built this way. Once every 30 minutes, they can do 40% more damage over the course of a fight. Do you balance a fight against their normal damage, and trivialize the encounter when cooldowns are available? Or do you balance a fight against their high-end damage, and make fights impossible when the cooldown is unavailable?
This may seem like a nonissue. Sure, most long CD abilities were struck from the game in 3.1. Furthermore, most long CDs don't equate to triple damage or a 40% increase across a fight. However, even things that increase damage by 5, or 10% across a fight, which aren't available on repeating attempts, can cause problems. The two primary examples that come to mind are Doomguards for Warlocks and Army of the Dead for Death Knights. Doomguards are a 60 minute cooldown that can increase your DPS by around 500 across a fight, a solid 10% increase in most situations (Maybe a tad less.) Army of the Dead can add roughly 100,000 damage on top of your total during a given fight with no opportunity cost, as it can be precast right before the fight starts, thus consuming no runes and no GCDs during combat.
Doomguards are being nerfed, both damage-wise and cooldown-wise, though their damage may still be higher than other pets and their cooldown is still a full 30 minutes. Army of the Dead has no such modification in store. However, I have a suggestion. First off, make it only castable in-combat. This means that you MUST dedicate 8 seconds and 3 runes to summoning your ghouls, time and resources that could have been spent doing something else. Second, retain their threat level so they're still a viable last second save in some situations, but halve their damage. That should mean that the cost of casting them in combat is relatively equivalent to the damage you could have output in the same time, especially when you take the loss of flow into account.
Overall, long CDs are bad. Take them away.