If SE was smart, they would release the new dungeons pre-made for the new battle system and everything involved in it. They said they are already aware of everything going into the new system, so the dungeons (And like I said, if they are smart) will reflect that.

About the geography, SE said they are redoing the maps, with that in mind, they will have the opportunity to create placement for these new beastmen strongholds they are talking about, and any of the new HUB's. These strongholds will most likely be new zones.