I have to agree with Terminal, a strictly system-to-system FTL really isn't the best of choices. Sublight velocities are simply too low. I'd suggest an FTL that can be activated anywhere, but has some extremely high risk involved. Say, a warp drive that can eject a massive amount of energy after a long journey, and thus direct jumps can only be made with individual ships. A fleet jumping in unison, however, would have to instead make regular stops to get rid of the buildup.