I think we all agree that the current system has some critical flaws:
- too much micromanagement with the different house types and the need to renew them to the new (and superior types)
- the need to connect to ressource nodes forces snake-like cities that try to cover as much ground as possible
- city spam is still possible and encouraged to take as much resources as possible
I'll propose a solution to this problems. My inspiration came from the asteroid fields in the GalCiv2 expansion DarkAvatar. In this game, you have asteroid fields away from planets, where you usually build upon. You can build extractors on those fields to remote mine them and then send the resources to a nearby planet.
I think a system like this would work perfectly with the vision the devs have of Elemental. Especially the vision to make the game look like a rpg world and not like the typical city spam you have in similar games (especially in Civ-alikes).
Lets take a look at a crappy mockup of the current Elemental map.

We can see the following resource nodes:
- a field for a farm
- a shard for a shardthingie
- a mountain range for mines
- a forest for woodcutters
- a lake for a fisher
With the current system, the smart way to build a city would be like this:

You build the city in a central location and then try to connect as many resources to it with houses as possible. Not only look those cities very bad, they are also bad to defend and need lots of micromanagement to function.
The micromanagement problem is the following. After you've built the city, you try to connect as many resources as possible to your city via the building of houses. Let's say we connect the field to the city and build a farm there, since food is very important in the beginning. After some turns, when our city has grown and we've got more tiles to build upon, we connect the next resource with houses, etc. etc.
Also we need to upgrade those houses to new types as soon as they've been researched since they new ones are superiour to the old ones.
All in all, the city above is ugly, messy and not much fun to build, since the design is forced on you by the need to get those resources connect to the city.
My solution to this problem is the following:

There are two key differences to the old model. Resources don't have to be connected to the city with houses anymore. Instead they are connect with roads. Also houses can be built next to resource nodes to simulate small shoves and villages that usually have sprung up next to larger farming or gathering places.
It works like this:
Resource nodes
- on every resource node inside your borders can the appropriate harvesting building be built on (may need a worker unit or not, debatable)
- those buildings need to be connected to a city (by a road, debateable) to bring resources into the resource system
- distance from the resource to the city has dimishing returns on the amount of resources harvested (this is to make super cities impossible) there are no penalties till a certain distance though (so that city spam won't be necessary to not lose too much resources)
Houses
- houses will be built automatically next to resource nodes in a small amount (those houses simulate the people working on those resources, it also creates the feel of small villages in a fantasy world, which is usually missing in games like this), amount of houses built depends on type of resource node and, if exists, upgrade level of resource node
- the population of those houses is added to the population of the city they're connected to (which means, buildings in a city that effect people also effects those remote villages)
- houses in cities themselves are built automatically too (very debatable, not necessary) or get built automatically in designated areas
- houses don't count as city extensions themselves, only special buildings do (like inns, armories, etc.), special buildings increase the build range by 2 tiles though, to compensate
- houses get upgraded automatically and require certain amounts of resources to do so, a global setting can forbid the upgrading of houses to help in times of resource shortages
- houses can be upgraded automatically till the level of house (hut -> shovel -> house) if the necessary research is done
- houses can be upgraded automatically further -> estate -> mansion only if for every estate 3 houses are available and for every mansion 3 estates (to prevent the silly filling of cities with estates, also prone to balance of course)
- huts have 5 inhabitants
- shovels have 10 inhabitants
- houses have 20 inhabitants plus 1 prestige
- estates have 20 inhabitants plus 3 prestige plus a slight increase in tax generated
- mansions have 25 inhabitants plus 5 prestige plus an increase in tax generated
Huts cost nothing to build, so if they're built somehwere you don't like, you can quickly destroy them, shovels and houses have a slight upgrade cost. Estates and mansions have a quite high upgrade cost, since they give much higher benefits. (All numbers can be changed for balancing of course.)
Well, that was quite a wall of text I'd say. Anyway, it is a complete revamp of the current system, but imho it would lead to a much more organically looking and growing world, would remove some annoying micro management. Would help against city spams and would free city designing from the need to only care about resource connections. This would open much more interesting city designs imho, giving players more abilities to make cities look like they want.