+1 for netstorm. It's great game. There's also fun game "StormMaster" (from early '90) that I think could be predecessor to NetStorm. Mechanics of the game is completely different, but also takes place on flying islands, and it's quite fun, too. You design flying ships from parts (and have to test-fly them), build them (there's nice economy in game - the real resources are ship parts sold between factions).
http://www.abandonia.com/en/games/426/Storm Master.html
Regardig base-building I've liked the best MAX (and to lesser degree MAX2). It's not really RTS (turn-based with optional almost-RTS mode), but base building is great - you have to scout for resources, build radars and various turrets to defend your base, and every building needs to be connected to others by pipes, or it stops working.