I too think the AI builds cities too close together. I think the easiest way to fix this is to increase the rate of Z.O.C. spear so we don't need to build cities so close together to grab resources.

The game's name should be changed to Spam A Lot.

City Spamming, it's not just the AI that spams cities, the gameplay requires it, want to capture a remote resource, spam another city, need a harbor near a shore hex, spam another city, want to limit other player access to a part of the map, spam another city, etc, etc.

Creatures Spam,  creatures over spawn in remote area's in long games.

Resources Spam, they over spawn all over the map, just research and wait for resources to start spamming, weren't resources so pose to be rare?

This is true, but the cost is largely irrelevant when the only reason you need cities is to snatch up resources off the map and to bring in more resources. Without snatching up the resources on the map cities are only good for troop production in Elemental as by themselves they don't produce much of anything except for a little bit of taxes. It's the rate of Z.O.C. spread that controls how close together you need to build your cities. If the Z.O.C. was larger you wouldn't need as many cities and they would be far more important. It's very fixable without the need to rebalance all the costs. The simpler a fix is the faster the Devs will be to fix it.

In this case as well Z.O.C. spread affects the game's pacing, so balance is an issue.

I don't think it would be that hard to fix.  Just add some sort of maintenance fee per city that increases exponential as cities are founded.  That would stop early game spamming because it would eat up all your money.  The downside is that this creates a limit to the size of your empire.  So to counteract this they could add another function called, for lack of a better word, "legacy".  As cities age there legacy would increase would inversely affect maintenance.  This would encourage a more thoughtful application of founding cities and would help discourage spamming cities.  Or you could just make npcs more aggressively attack weak cities.