Personally I think they need a darkcloud/nyzul style dungeon system into the game. They already created dungeons with multiple paths so they can make HM versions later, why not make 3-4 paths that vary based on intersection with bosses and when you enter a dungeon it is 'set' to a specific but random path. The key is you are not allowed to choose the path so you can't just always pick the most mind numbing but efficient one. Mobs in those random paths would also not always be the same amount or clustered exactly the same but had an easy variable algorithm that they could test the content.
As others have pointed out the key issue with the dungeons is the mind numbing and linear focus they became in this game. I don't want them to lose the meta game surrounding the duty finder, but when you go into a dungeon you shouldn't always know exactly what to expect, only what might appear. That slight change would, in my opinion, greatly reduce grind fatigue those types of dungeons give and keep players focused on playing the environment rather then playing the wheel of efficiency at least for a time. I would also love a bit more randomness in the boss fights as well, I actually appreciate the final boss in Stone Vigil HM for instance because you were forced to pay attention to animation and recognizing move types if you wanted to avoid damage as other then the split off, nothing was timed, and nothing was hp based.