You can very easily put the city spam option to bed, because you can mod the minimum distance settlements must have from each other. The default for human players is 5(!) hexes. You can change this to any desirable number, say, 11 (or even more), making the spam impossible, because you cannot squeeze them anymore.
The downside, if you can call it that way, is that the builder-fortress is, under this rule, a settlement as well, which means those fortresses become mostly obsolete. (In single player this is actually no downside at all, mind you, since the AI cannot handle builders anyway.)
The one thing that is missing in AoW 3 is a separation of builder-built Fortresses and settlements with regard to this moddable feature.
Admittedly, being forced to "mod" something has a ring of "playing a different game", and that and other issues have been discussed with the devs already, but I think one have to accept the point, that if you have half a million and more buyers of a game, a lot of those are playing the game more casual than the hardcore gamers playing all the time and multi or PBEM, finding ways to exploit the system the majority of the players wouldn't dream of trying.
So modding seems the only reasonable way to go, especially when you count in the various options you have when setting up a game. Starting conditions, map size, richness, the amount of sites, terrain and so on, all that has an impact on how the game plays and how you can "beat" it.