This could go somewhere interesting, I think, with better UI and gameplay tweaking.
The ship-building could greatly benefit from some UI refinements such as displaying a preview of the ship you're building at all times, flagging when you have a synergy or not, and allowing viewing all of the part type lists at once (rather than having to exit out to check if you have a match).
Controlling the entire fleet with one cursor was a really interesting challenge at first, but then as the lasers got longer-range and the ships got faster, "hold still in the middle" became a better strategy.
And if the combinations somehow visibly affected gameplay, that would be cool and tie it together better. (Ghostly alternate universes with ships taking different routes?)