Though maybe they could go a general "Evil" team this time and make a team that simply wants to destroy the region and remake it again using Kyogre/Groudon. Both could be used for the Mass Destruction purpose, almost better than the Space/Time/Void trio and the Tao Duo Dragons (I still wait for canon proof that Kyurem is more than just some Mew/Ditto relation to Reshiram/Zekrom. It being a Space Leech thing doesn't help....PokeCell wannabe.) They could literally destroy the regions just being awake.
It would be almost the same thing like original Ruby and Sapphire but with more evil teams. Proper sequel needs to be better than that. It's doubtful if it will be ever made.
And think about it - how could someone remake the world if everything would destroyed by drought/flood? It doesn't make sense. If it would make sense, Magma/Aqua would be pure evil in original games. That's why Magma/Aqua were more composed compared to other teams. And that's why they didn't want to totally dry/flood world because they knew it would be impossible to change world after that.
They can't use unused space but they need unused space?
B2W2 really didn't follow this. The airport town, Rebirth Mountain, the new 8th Gym city. Those are all within a very small section around Undella bay and there wasn't that much space there.
How did I contradict myself? I said they can't put too much cities in unused areas because they need to keep some distance between already existing cities.
Look at map of old Unova from B/W. Free areas were bigger compared to those in other regions. Unova is the only region so far designed to have new cities in sequels. Other regions are too crowded already.