They should get rid of the timers, implement a point system where achieving specific goals and defeating enemies will give you certain amounts of points. Hell, even make defeating enemies in certain zones a goal, and perhaps give more points if they defeat the enemies within a specific time.

At the end of the dungeon, they can spend the points on items. Based on performance, they may or may not be able to buy certain items. This means there is always an incentive to doing the dungeon, no more of this "Well I have (insert class here) so i deserve that item!" It would be based on party effort but in the end, given that enough points have been earned, players will be able to come out of the dungeon with the desired item(s).

This idea will make every room of the dungeon worth the stay. Make puzzles in each room, make goals.