The original Starship Builder prototype suffered from some terrible user interface choices. It's not that they were stupid, but that they were a product of tacking on lots of features and not being sure about how I wanted the game to play. Now that I have a better sense of what the game will be, I can greatly improve the user interface.
This past week I've been working on the in-game controls for commanding ships. Since I see no need to reinvent the wheel, I've modeled the controls after typical real-time strategy games like StarCraft and, especially, Company of Heroes. Like most RTS games, you can left-click on a ship you own to select it, or drag a box around several ships to select all of them. When you have ships selected, you can right-click somewhere in empty space to order your ships to move there. I've stolen a feature from Company of Heroes, whereby if you right-click and drag you can easily reorient which way your ships are pointing.
The green circle in this screenshot indicates that the starship is selected. The green "ghost" indicates the destination to which the ship has been commanded. The thick green line indicates the path from the ship to its destination.
As in the original prototype, once you have commanded a ship to move to a location, an algorithm will determine the optimal "activation level" for each thruster on your ship. This algorithm I was able to lift virtually unchanged from the original prototype.