Fenixp: See, cooldowns are an attempt to balance spells. Mana points are also attempt to balance spells. Combining the two is utterly redundant and unnecessary if you design your system well enough - cooldowns are literally a way to fix a problem with a piece of duct tape instead of actually fixing it.
There are a couple alternative approaches as well:
1. Balance spells against physical attacks well. Physical attacks would work well against single enemies, with spells doing less damage, but capable of hitting multiple enemies, for example.
2. Decide that physical attacks are not going to be a primary means of combat. In this case, there would be no dedicated fighter characters, and everyone would be using spells all the time.
I should point out that there are some effects that simply can't be balanced without cooldowns or some other strong limitation. Romancing SaGa 2's Quicktime spell (appearing later in Romancing SaGa PS2 with the English name Hasten Time) is an example of a spell that pretty much needs a cooldown to be balanced at all; otherwise, the player can just cast it every round and the enemies will *never* get a chance to attack. (In both the games mentioned, it is actually quite easy to kill the final boss (in RS:MS, the strongest version) with this strategy, though in English RS:MS, you need to do some tricks to ensure that you don't run out of BP or Chalice DP.)