Something in another thread inspired me to look at Elemental in a different light by comparing it to the other TBS I've played. Unfortunately it seems like all the TBS I've played were developed by the same people, haha. Master of Magic, Civ2, Colonization, Alpha Centauri, Civ4, Civ4 Colonization, and GalCiv 2 (Total War would be a bit of a stretch). After looking at these games, I have to say...
I REALLY don't miss taxation. I didn't even notice it was gone at first. Every TBS has it (wait, I guess Colonization didn't have it, except in the form of the King taxing you), and thus also has City happiness, and it's usually annoying to manage. Unfortunately, it also simplifies the empire building a lot, but quests take up the time that is freed up. Anyone miss this mechanic?
Population directly affecting production stats, such as hammers, coins, and food, thus more population results in more production (and more taxes). It seems like the only point of your population in this game is to upgrade your cities to better levels to gain access to better buildings, and to provide people for your army. To me, I would think that more people would result in lower build times (more laborers), and larger effects from your buildings (example: more researchers in your archivist building results in more research). Maybe it could be made so that, say, for a lore shop you get 1 arcane research point for the city level (level 2 city -> 2 research points). Only applies for those 1 per city buildings, so doesn't apply to Lost Libraries. Opinions?
Government types: another way to interact with your empire's population, which the game seems to lack right now. Are you an oppressive dictator or a light-handed president? Although happiness management was annoying, getting rid of it lost a lot of depth in the empire part of the game. So the game is simply using people to support your questing instead of building a civilization for all of your people to prosper.
It's late so if I think of any others, I'll post them later.