So what? The problem stays the same - outside of combat cooldowns have no mechanical effect - they merely annoy the player.
They can annoy the player, but typically the longer cooldowns are for the more ridiculous powers. In terms of WoW, though, I think the only cooldown that typically ticked me off was the Heartstone. The other ones, I just typically used something else. Of course, I typically don't play classes with a lot of spells either.
In combat cooldowns can only work if they are at most as long as the longest combat and not always even that - if the battle dynamics relies on cooldowns too much it just means that running around like a retard turns into a bizarre equivalent of FPS popamole.
Actually, they work beyond combat as I've mentioned above. If you're in a dungeon, and you're spanking the critters up to the END BOSS of DOOM, you might decide to use a 10 minute cooldown AoE attack to clear the way to that boss only to have it unavailable at the boss. Now, you can argue that you're just going to sit there and wait for that cooldown to attack the boss and that's annoying. Then again, that's not a problem with the mechanic, that's a problem with you or the people you're playing with. The one reason I thought the Leroy Jenkins video was so funny. If you're spreadsheeting that much, you're not really playing the damned game. If you're waiting around for one attack to cooldown as opposed to using another method while it cools down, that's either on you or the game itself is poorly designed. That wouldn't be the fault of the mechanic.
It's just like saying turn based sucks because you can choke point a door and just shoot at the door because everything has to wait to come through that one door, one at a time. I can name several games where the turn based doesn't work well. Even if it does work well over all, there are maps where it doesn't work well. Fallout 2's Enclave location, for example. You can kill the entire Enclave at that location about halfway through the game because of all the door choke points. The combat in most of the game works really well, but that location is easy to exploit just because of the map.
Even if they do work, they just work like regenerating mana bar, but with only one spell worth of mana, less timing and no resource management.
Actually, all timing and the resources you manage are your abilities.
Also, most games that rely on mana also have mana potions or other ways to quickly regain mana. So, you can argue that just forces players to take up inventory slots.