I went back through my cities and I think you've won me over, with a couple of caveats.
First, I think their is some ambiguity as to what exactly constitutes a region. I'm viewing Scalestander Port as straddling 3-4 of them, one forest and the rest plains. Wallstander Village lies across 4-5: a forest, barren plain, grassy plain, and one or two mountain, depending on where the boundary might fall. Grasschopper Port is was my first city and is just absurd. I'm currently leaning towards the idea that cities in the 1500-2000 range should be scarce. Your capital and maybe one other large trade and manufacturing center in a large kingdom, supporting by a network of 8-10 smaller settlements. I think most should be in the 150-500 range.
I'm with you on rivers and coasts forming great natural borders. I think a good system could have you settle a single region, consisting of an area about the size of Wallstander Village (ignoring the region boundaries on that map.) Selecting a site to settle would highlight the region claimed, making explicit any borders not already obvious from a coastline or biome change. You could then claim two adjacent regions fairly early on, with the others accessible later.