I haven't put as many hours into the new Elemental as I would like to have (kids 'n stuff y'know?) but I'm already finding it a dramatically more engaging experience. I used to have to TRY to have one more turn in Elemental. FE has me merrily bashing the end turn button 'just one more time'. I have a few suggestions, some of which may be born from a lack of knowledge of the game, so please correct me where I am wrong.
Would be nice if you could re-arrange a city production queue by drag and drop. Save deleting and re-queuing everything.
Mouse over buildings in the city could tell you what those buildings are. Sometimes I just like to nosey around my pretty little city and I don't really know what most of what is. Mouse over could display the stats of the building as well. What it contributes and what it costs etc.
Means of travelling over water would be hugely appreciated. I get hemmed in by rival borders quite quickly and it's pretty annoying that I can't send ships of pioneers out.
The price of gear for your champs is pretty outrageous. One set of leather armour shouldn't bankrupt a healthy civs 150 seasons of treasury.
Can outclassed monsters ever flee from your army or even offer to join you? That would be cool...
Space bar or something to end turn would be nice. I'm lazy... 
A method of converting null production into growth/gildar/other resources would be great. I know there are buildings that allow this for some resources, so maybe I just haven't got far enough in to experience these other resources.
Game difficulty only seems to modify the difficulty posed by the other AI civs, not wandering monsters who are a little overly formidable in the early game? Would be nice if easy mode also made wandering monsters/lairs easy-mode. A lot of the time I do like a challenging game, but sometimes I just want to smash everything and feel tough.
Edit: Oh and units should be allowed to hit back once per combat round.
But the bottom line is... Way to go SD. Really liking your comeback here.