Ladies...
I thought it was clear from day one that the game will have cooldowns, so I don't understand the sudden "oh noes! the cooldowns are in!" cries. Is
Roguey the only one with brains here?
It was clear (I hope) that the game won't use the Vancian system, which isn't a huge loss as it was never implemented well (definitely not in the IE or NWN games where the formula was rest, blast your foes, rinse and repeat). It works like a charm in a controlled environment (PnP) but not in cRPGs where little Johny's feelings must be taken into consideration. Sad but true.
So, if not memorization, then what? A pure mana system a-la Diablo? Sure mana-based casting worked well in the old games like Realms of Arkania where magic was going up slowly, but in modern RPGs (and PE is a modern RPG whether you like it or not) it goes up fast and you get a steady supply of mana potions, should you find the regen rate too slow.
Therefore, the cooldowns are the only options here. While they are mostly associated with shitty MMO and "watch the cooldowns" mini-game, there is no reason to believe that they can't be done well, because in a nutshell, every magic system is designed to restrict spellcasting in some way. As Feargus pointed out, DnD's X number of use per day abilities are nothing but very long cooldowns. From this point of view, cooldowns definitely work and they can work very well, as long as they aren't too fast.
Of course, Obsidian will most likely try to make combat actiony, but we knew that from day one when they said RTwP (i.e. cooldowns have nothing to do with it).