While I agree that elevation can have some influence on city generation, I also think that can be taken into account by the person doing the generating. If you specifically want a city on a hill, then arrange the roads and such where you think makes most sense. If on a cliff side, then perhaps make it in layers showing switchback style roads (or else use a different generator that can do a sideways view at a vertical city). If you REALLY want to add the lines, perhaps import the map into something like photoshop and add some basic indicators for elevation.
THAT SAID. On the other side of the argument, perhaps an easy-ish addition would be a draw tool that doesn't affect the map or its generation. Basically a new layer which can have basic shading to indicate elevation. This would be helpful in late stages of city tweaking. Having a basic draw tool to show an edge of a cliff, or steep hills, etc, might be nice. I'm thinking of places like Jerusalem. Technically elevation doesn't play any significant role in the city itself, but one side has a steep almost cliff face. That could just be added in photoshop, but again, perhaps a bonus for premium users?