Thanks for a long and interesting post, sorry for not replying to it earlier! Answering to your question at the end of it: some of your suggestions can be implemented and the others... can be implemented too, but not in this life :)
First of all please note that this generator doesn't try to model a city. It just generates images which look (from afar) like maps of medieval cities. For example it was too time-consuming (for me to code, not for the generator to generate:)) to create realistic layout of small streets, so instead I used simple randomised bisecting of blocks to create an appearance of chaotic alleys. And it works if you don't look too closely. As a matter of fact there are no individual buildings, only plots of land. That's about "small castles", "noble dwellings" in slums etc. I hope to add houses to these plots later, but I don't have a clear idea how to do it yet. Then I will assign functions to all them, populate them with citizens, create biography for every citizen etc :)
- Local temples and fountains. As I said currently there are no buildings except the main temple and the castle, but since I have the main temple, I can appoint one of larger polygons inside a ward to be a local temple with a small square in front of it and a fountain/well. It should make ward layout look more... meaningful?
- River and canals. Yeah, I was going to place the river outside of the walls. It's an interesting note about one bank being muddier than the other. I just couldn't remember any city with a large river going through the walled area. I'm sure people will ask for such option :) Neither I remember a city with a network of canals. When I say I don't remember this or that it doesn't mean I don't believe it happens. It just mean I don't have a picture in my mind and because of that it's harder for to reproduce it with the generator.
- Towers. I can't remove most towers, because without them the walls on the map don't look like walls :)
- Multiple walls. That would be nice. The problem is that as far as I can judge, my cities are just too small, much smaller than real cities were. Even my "large cities" hardly have place for multiple rings of walls. I need to think what I can do about it...
- Harbours. Yeah, I think that's how they are going to look more or less. Except walls. Were they walled at all?