Watabou, I just stumbled across this thread and I've got to say... I think you should really reconsider the idea of City Painter, or how some of its features could be integrated into Generator.
In short, the ability to draw in some presets (like a coastline, roads, or the course of a river) and then let the procedural generation take over, would be an incredibly robust tool and really interesting procedural generation.
The longer version:
I have been using/evangelizing your generator for a while, and I want to just emphasize I think it is an absolutely genius piece of work and an amazing thing you've built for the community.
But as to why City Painter intrigues me... sometimes I have a particular area in mind (like a city that has a natural harbor, is on an isthmus, at the fork of a river, or is at a crossroads, etc.) that I want to roll a quick map for. City Generator isn't great for that kind of task, need to do either a lot of rerolling, Photoshopping, or fiddling with the warp. Usually, I stick to using your tools for cities and settlements that are geography agnostic as a result, and do this "specific geography" settlements by hand. However, playing around with City Painter for a few minutes, it is an absolutely amazing tool.
Being able to set the underlying geography, then "paint in" procedural buildings and blocks is awesome. All it is really missing is a way to do rivers (though perhaps I just haven't figured that out yet) and more intuitive means of export.
Gravy features would be new "brushes" for things like " shanty towns" (small buildings, high density), a "docks" that autogens docks in an adjacent water tile, and perhaps a mixed edifice-borough option for generating one large building, with smaller surrounding ones.
But really, even if if it were just somehow possible simply to predefine geography (land, water, rivers), and the options you have as path in City Painter, in City Gen, and then you let it fill in around that stuff that would make this suite the be-all-end-all as far as I'm concerned.
Again, thanks for all you do, amazing work.