There should be a grading system at the end of each dungeon run. Grades vary by number of mobs cleared. It could also be percentage instead of grades... the higher your percentage/grade is, the better the extra reward (gil, craft mats, etc.) This way, if people want to speed run, they can do so and get a minimal %/grade with minimal rewards. For those who choose to run the full dungeon can have better rewards. It makes everyone happy.