It’s been some time since we did not play a RTS. I’d vote for Star Command: Revolution.
Unlike other strategies SC:R provides a non-linear campaign where missions can be taken in somewhat arbitrary order. Player controls a mothership which can build bases, which can in turn produce ships. The game is divided into interconnected sectors—each of the sectors is a mission. The mothership is the only unit that can move between sectors.
This particular style brings a lot into the game as resource management becomes crucial since amount each of the five different resources follows the player from sector to sector. Overspend in one mission and you may have blown your game unless you can find resources elsewhere.
The game features four distinct races (less varied than in Starcraft though) and the player progressively obtains technology for all of them.
The game also supports multiplayer for up to 4 players.