I was reading under the post about flying structres (cities/castles/etc...) and I had an idea.
I know in the original MoM one of the many things that made it interesting was the fact that there were two game worlds per map connected with the Towers of Sorcery. I understand that does not make any since in Elemental, but I did consider the strategic complexity of it as interesting. That being the fact that you didn't simply have your own borders to worry about, your borders existed in other directions, making it more interesting.
For instance, think of the land map as a 2d map. It's played on a flat level with moves etc. However if flying areas were implemented, or even better, possibly Underdark elements, the map would then become 3d instantly. If caves also were intrances to the underdark then you would have additional problems in early game. Late game with flying and the colonization of the sky with flying cities would be similar to Civilization when you get access to Galleons and find the remaining continents. Perhaps even races could be implemented to take advantage of those environments (Dark Elves/Illithids/Dwarves for Underdark) or (Cloud Giants, Winged Elves). Actually the underdark portion lends itself a lot better to the idea now that I think of it. Cities in the clouds are neat to think about but civilizations that have nothing to do with the earth... hard to imagine.
I think this is most likely something that could not be implemented in the first game, it seems to large, but perhaps later. It would make for an interesting expansion. I know in most D&D literature surface dwellers are always having problems with things crawling out of the depths.