Children of a Dead Earth is amazing fun. Difficult, but very fun.
Other possibilities include Stationeers, if you're into that sort of game -- incredibly complicated electrical and gas systems are possible, along with custom-written logic to maintain it all -- or Command: Modern Air-Naval Operations, which is likewise incredibly complicated. The latter has a new version being released sometime in the near future.
Never have tried Rule the Waves, but I'll have to give it a look.
But god I want so badly to play C# Aurora.