D&D has always sort of had cooldowns - Vancian magic.
The mechanism for WoW cooldowns is rather different from D&D encounter powers though. Cooldown times vary greatly, from 6 seconds to days, and there is no need to avoid combat for a time period, the cds regenerate no matter what you are doing. For instance a WoW power with a 5 min cd could potentially be used twice in a boss fight.
I definitely don't see encounter powers as a WoW-ism. WoW has no concept of the encounter.
This is where I think a lot people disagree with each other.
To me, and I suspect to many others who think the comparison is valid, 4e's at-will, encounter, and daily powers seem very much like CRPG/MMO power cooldowns, and much more so than 3e did.
I'm not an expert on WoW, but having played a decent amount of Guild Wars in my time, I can say that it feels very similar. You have your powers you can spam more or less all the time, your powers that you can pull off periodically in the fight, and powers that you can only pull off once in a fight, all achieved via cooldowns. Obviously 4e scales it slightly differently (and for all I know, WoW might too), but it still seems very comparable to me.
The reasons I
don't think that the same can be said for 3e and earlier are twofold:
First, it didn't apply to every class. Spellcasters had a cooldown mechanic via Vancian casting, but fighters and thieves didn't. This is in contrast to CRPG/MMO practice where it's a defining characteristic of the entire combat system.
Second, there were no tiers of cooldown. You cast your spell, and couldn't cast it again until the next day. A defining feature of the MMO combat being discussed is that different powers have different cooldown times, which becomes an important tactical element.
Basically, while you're correct that 3e had some MMO-like cooldown aspects, I feel that 4e is MUCH more similar in that regard. Not identical, but much more similar.