I don't get the Civ hate shortly followed by MoM praise.
What I'd like more than anything: a clean interface like Civ 4/5; a combination of Elemental and MoM features, exactly which are debatable but definitely the M:tG inspired spells from MoM; more strategic and tactical options; and some real consequences for actions.
No offense meant to StarDock but the interface in Elemental is still a little rough around the edges. Civ's interfaces may not be perfect but I found them very easy to use, most of the time, and that's all I ever ask. There are a number of suggestions out there to fix Elemental's interface already, so let's not go there now.
I understand not wanting to be compared to MoM all the time but it's a classic. You can't go wrong combining Civ1; RPG heroes, battles, and enchanting; and M:tG's unbalanced spells. Elemental has most of what MoM had and more but it's just not fleshed out as well yet.
As for strategic and tactical options, it'd be nice to be able to do more than just attack and defend with armies. The weapons and armor just seem to have different numbers so I only worry about getting a bigger number. The sames goes for spells, and army sizes. It'd be more fun, and meaningful, to have choices with both bonuses and weaknesses. The rock-paper-scissors mechanic may not the best but it's better than just upgrading to weapon/armor/spell/summon 2.0. It'd also be awesome if I could hide my units and lay ambushes but that's a bit harder to add in at this point.
Finally, I wish games like this had more consequences. For example, raising and lowering the land is pretty cheap and we can even raise volcanoes. Amazing! But, I'd like to see what would happen if raising a mountain range to keep out your enemies caused a shift in the weather and your lands dried up. What if that volcano lowered the global temperature or you had a spell to halt the eruption and use the new found minerals to create a bunch of fertile land? All of that'd be cool but not at all easy to design, balance, or code (weather, ecological, and economical simulation, all at once? No problem, right?).