First off, I just want to say that I love the huge scale for Sins, but there is one thing that bothers me, the predetermined phase jump routes. I wish that I was able to form my own routes.
For instance, imagine if the scout frigates had the ability to scout out new routes that other ships could then use. Of course, attach an appropriate cost to it and make it take a good amount of time.
The only restriction that I would keep is that when traveling from one star system to the next, you have to travel to that star. You can't go straight to any planet of a different star system.