No matter what system you end up using, taking a look at GURPS space is definitely a good use of time. It is a great sourcebook, with lots of good stuff to think about when setting up your universe.

Since you seem to be interested in some crunch with building/customizing the ship, I don't know that FATE would be a good fit. Gear in any fashion is not its strong point. I have been doing a lot of FATE personally because it is so easy to jump into playing...but it isn't really a game, it is a toolkit to build your own game.

Alternity probably would get my vote. The feel of old school traveller without the clunky old system.