Would you waste time after every battle for 10 or 15 minutes so you can use Fire Armageddon the next battle and finish it less than a minute faster than if you had used weaker spells?
agreed, a player who understand and use the game mechanics effectively, will exploit these system, no matter what limits are introduced.
A mix of both could be usefull. Long cool-downs for high level spells and some portions to reset or shorten the cool downs. So you have time(spell) and resource management