Sins was good for a while
Come to think of it i haven't seen many space based RTS in the past several years. I remember a few star trek ones back in the day - Armada maybe?
They're all the rage lately.
There have been a few on Kickstarter and some looking around on Steam Early Access.
Plus earlier this year (or late last, I've lost track of time) we had Ancient Space.
I thought Nexus: The Jupiter Incident was a pretty atrocious game. Each to their own I guess.
A much deeper and more tactical game focused around small numbers of large ships with some customisation ability.
My main issues with it were a horrifically terribad storyline and the near requirement of 100% foresight to predict exactly what equipment you need on the exact ship for each mission... felt quite apparent at times, especially when going back and reading over mission FAQ's.