I think some of the posters don't quite get it.
First, reloading a weapon isn't quite cooldown - it can be initiated at will, which is often important with multi-shot weapons and it doesn't go in the background (as some hove observed), maybe outside of some ancient games where you had single reloadable weapon in whole arsenal and it was mostly a gimmick (see automag in Unreal) and outside of HL2 which is hardly stellar in terms of its firearm mechanics. Even in those games this wasn't terribly exploitable, as switching weapons took time and there was little no point to switch weapons from what was currently preferable due to mechanical or ammo considerations.
Second, the problem isn't using something like cooldowns where it evidently makes sense, it's slapping the timer on everything and calling it a day. If you have something that should logically work like cooldown, then, by all means make it work like one. If it shouldn't logically work like a cooldown, then fucking don't make it do that.
Third, if you need some time management mechanics, then it's usually far better to put this delay *before* using the ability, not after. Most stuff person can do takes time, casting magic is usually portrayed as using complex rituals that take time and so on. It makes little sense to just fire off your spell, then sit on your ass twiddling your thumbs because the timer says so. It makes a lot of sense to actually spend time *casting* this spell, then be able to start cast it again immediately after as long as your resources allow, because why the fuck not?
Additionally, introducing pre-ability delay allows you to make it far more of a factor than some cooldown that may well go into effect after your enemy is dead. For starters, the enemy may attack you interrupting whatever you do, or at least causing shitload of damage. For this reason some abilities, even weakish and inefficient may be preferable in some situations, if only because they cast fast and will actually have chance to go off without being disrupted. Additionally, other abilities, not necessarily useful in their own right may come into play to buy caster some time before he can launch his nuke. And there might also be abilities to counter those.
Fourth, cooldown mechanics, right from its start in hazy early nineties (LoL1, etc.) has been resembling QTE. There is no denying that and it makes for some mightily shitty combat. If all abilities are on separate cooldowns then it makes sense to just spam whatever is available ATM. If LoL1 didn't have it's particular kind of charm, not without help of musics and pretty pixel art, then it would be a horrible piece of turd, far worse than fucking oblivious.
Fifth, cooldowns are probably the worst way to introduce any additional complexity to your combat skill use. Not only do they work poorly in this regard, but they tend to not make sense and supplant far better alternatives.
For instance Call of the Ancients literally calls down the four barbarian ancients to fight alongside you. How would that work if it was spammable?
That's actually a no brainer.
You logically can't call multiple copies of ancients at once, so spamming would only accomplish unsummoning and resummoning, terminating any actions of those summons and resetting their position - why would *anyone* spam that?