I think it would be pretty cool if the next deep dungeon focuses on exploring the rooms in the floor to obtain permanent power-ups and the tradeoffs between them. Something similar to WoW's Torghast anima powers (Which in my opinion was the only fun part of the whole experience)
Imagine if you explore the floor as a black mage and get across one that offers you two options like "Your casting speed is reduced by half but the potency is also reduced by half." and "Your casting speed is increased by half but the potency is also increased by half"
Some job-exclusive power-ups and general power-ups with the tradeoff being in the power-up itself or in choosing between one of the two.
Yes, balancing will be totally broken, with things like tanks getting some power-ups and ending up having self-heal better than any healer can provide, or healers dealing damage in numbers bigger than the DPS. But I believe this is why I like the idea and why its fun. It's a system that is meant to be broken without affecting the outside environment of the game (You leave the instance and lose your power-ups. Nothing such as carrying them to dungeons and trials).