While we don't want to copy Civ wholehandedly, we also should recognize that Civ does, in fact, do some things well (and possibly, right). We shouldn't be afraid to take cues from Civ and twist them to fit Elemental. After all, if you want to be picky about it, Food in Elemental is exactly the same thing as Happiness in Civ 5, save for the fact that Food is a hard cap and has no secondary benefits.
That said, terrain does need to be a little more 'alive' in the sense that it at least partially influences city placement and development. As is it, there's no real choice or decision making in city placement. It's merely 'find resource, drop city'. There's just no incentive to expand vertically or horizontally; bigger cities don't get you anything special and more cities are -always- useless unless you're spamming them (which is essentially the same as spamming buildings in fewer cities). While the game has limited the ability to city-spam, it's still also not rewarding city building either. Anything you'd really want is available at city level 3. It's not that 4 and 5 level cities are hard to get... it's that there's no reason to get them. Right now, I can build 4 cities with 2 workshops a piece and be pretty much set for materials for the majority of the game; there's no pressure that I need to expand. I have no reason to expand (and even things right now like maintance are easily overcome - I have one game where I'm spamming buildings and have 0 gold mines, merely a swam of merchant champs.
I'd say that one place to start off would be to give terrain some trickle flow of production, resources, as well as population/housing modifiers and prestige. Building a city near mountains or woods might give some modifiers to unit and building production while plains would allow for 'bigger' houses (modifiers to how much each hut provides). Resources might not be a profit persay (you gain X) but rather, a sort of discount to existing buildings (so you have to actually build something to get something). So mountains might provide a bonus 0.2 material so workshops (or what have you) produce 1.2 base instead of 1; not much, but a heavily mountainous region combined with a high level city and a handful of workshops will probably get you a heck of a lot more material with a far smaller cost than simply spamming workshops. No one really likes living in a swamp (even if the houses are nice) so prestige might drop by 0.1
Then also decrease the amount of stuff resources give (maybe even a dramatic decrease in how much each resource node provides but a slight increase in how many of them there are) and increase costs and upkeep. Make production times higher. Also add in high (4 and 5) city buildings that really help out with an associated very high costs. Perhaps even some nice unique (faction or world) buildings that depend on both high city level and terrain. Make existing high city level buildings provide better percentile bonuses. Move more buildings to rank 4 and 5.
Heck, one could even have effects related to combat. For instance, swamps might decrease the effectiveness of soldiers trained there... but provide access to unique units. This is another thing that Civ5 does well; there's cool resources that let you do neat things. More of these types of 'special' resources would help as well - if there's a neat special resource out in the middle of no where, should I drop a city there even though that city really won't be good at anything (and take a while to get to a point where it's making some sort of profit). By special, I don't just mean crystal and metal - I mean fancy cool things like the currently rare horses and wargs. "You found an shrine to an fire elemental. If you build X, Y, Z here, he'll power the forges and people let you produce soldiers that have a flame aura!". "You found a hidden glade in pre-Catalysm forests. The magic here is strong and you find that soldiers who train here become almost bear like. You now have access to Bear-zerkers!"
This would be a start to making cities feel different and also, in part, make terrain influence city development. That city in the middle of the plains (ie every capital city in every fantasy movie ever)? Yeah, it's gonna be huge with a big population. Those highly productive but slummy mountain towns (again, in every fantasy movie ever), likewise. Do I place a city here and get a little more production and defense... or do I place it over there and get more prestige.