Encounter difficulty is a function of both player strength and enemy strength. You can't assume that simply because players have access to ability X, all PVE encounters must be easy. What if Ifrit had an ability that he uses twice per fight that is guaranteed to one-shot the tank unless he has Invincible on? What if he also regularly wiped his hate list? Suddenly the FFXI Invincible on a 15 min cooldown doesn't sound that backbreaking, now does it?
I think you're looking at this from an irrelevant perspective. It doesn't really matter how strong they are in relation to their cooldowns. Long cooldowns on useful abilities are always detrimental to game balance simply because they create very infrequent spikes of player power. The encounter designers have to then decide if they want to balance the encounter around people having the cooldowns ready or not. It should be obvious why this is bad. Additionally, PVP content is coming and people aren't going to like fights always being decided by who has more super abilities ready.
