I say we work with Star Systems.

For FTL, I don't think we should do Warp Gates or Hyperspace. I think it should be some sort of system that requires considerable preplanning to pull off successfully and safely, with sending Drones to test routes or something. The point is, it's not something you can do on the fly if you want to show up safely and anywhere near where you want to be, so no fleeing mid battle.

By the way, an Idea, the Beacons.

A method for determining you're location in Space. Many major planets have a Beacon. The Beacon's are perfectly synchronized. Every (Let's say) Hour, each beacon sends out a powerful Light Speed Transmission consisting of the name of the planet, and the current Standard Galactic Date/Time (However that is measured. Pretty much the Sci-Fi equivilent of Greenwich Mean Time). If a Ship wants to determine it's location in Space, it listens for Beacon broadcasts and compares the current SGD/T with the one in the Broadcasts, a quick calculation involving the Speed of Light should tell the ship how far away from that Beacon they are. They then do this for every Beacon transmission they receive and, by consulting a decent map, they can use the distance to each beacon to determine their exact location in space.