I really like the color scheme as is, but if you want a bit more color you could do some muted dark greens for trees and grassy areas. For the circle in the eastern part - a temple? Tower of Sorcery? Great library? Mysterious ruins of some ancient civilization?

For name, City of Thunder Rock sounds slightly better to me than City of Thunder Cliffs. But I think Thunder Cliffs, on its own, is a perfectly fine name for a city.

I love the idea of having some secret passages from the cove into the city. That's especially good for in-game use; you could even create a map of the storm drainage system (or whatever it is) and overlay it on the city map for game purposes. The size of the city would easily support an entire urban RPG campaign.