I was thinking about this earlier, and I was wondering how hard it would be to solve this issue by allowing users to regenerate individual patches and/or features along already generated voronoi lines? Ex: changing from a farm field to housing, or adding a road along a line between tiles that already exists. It would be like a manual override, where the generator fills in the rest.

Another option could be using a system, much like how ProbableTrain has their city generator set up, where a user could make changes to the voronoi layer and designate any manual changes before the generator kicks in.

Also, I am really hoping that the island idea you have is going well. I've been trying for a while to manually make an island citadel which connects to the city via a bridge.