I think the most interesting land system I've ever played was Age of Wonders climate system. AoW had a lot of empty land spruced up with cities and capture points, but the land itself still had a large impact on the game. In AoW, crops only grew in certain climates based on race and military units got morale penalties/bonuses depending on land.
For example, Frostlings grew crops in the ice, got bonuses in the ice, had creatues that hid on the ice, and had spells that turned land into ice. As they expanded their conquests, what was once desert and grassland got swallowed up by frost and it added immersion to the game - you weren't just fighting the Frostlings to defend your city, you were deploying magic to resist the encroaching glacier that threatened your army and economy.
How could we adopt this in elemental? We have 10 predesigned factions, many of which could have land based 'themes' from what the limited backstory we have in WoM.
Tarth - Swamp
Gilden - Mountain
Yithril - Barrens, desert?
Magnar - Defiled land
Paridan - Rejuvinated land
You could have maritime, steppe, winter, etc. themed civilizations. If you don't want to go that route, you could leave all the civilizations essentially equal but have magic work with the land. Let factions with 3 water shards turn their land to swamps and expand oceans, let them create Frost Elementals, Swamp Snakes, and Giant Squid to fight, etc. If you wanted to be daring and take a chance, there are a lot of things you could do with the elemental engine to take the game to 11.