One point to consider is what you're trying to represent. If you're trying to represent a teaching aid to show history or to show current limitations, then a 3D representation might be a good one. If you're going for a day-to-day use map, what you're using for FTL technology will make a big impact on what you should show. If you're using something like wormhole or stargate technology where the routes are fixed, consider something like a subway map (a very abstract representation of the routes). If your technology is "simple" FTL where you can go X amount faster than lightspeed, then you're going to have a fairly dense 3D map that's pretty much point-to-point and something closer to the abstract list that Hai-Etlik suggested would be more appropriate. "Subspace pathfinder" technology (ships travel through a different kind of space and it's cheaper to go through an already-discovered route) is a nice middle ground where both kinds of maps are appropriate: a 3D one for route discoverers and a subway-type or list-based one for regular users.

Think of traditional maps: traders and sailors use one kind of map that's adapted for their needs. Teachers will want another kind of map, and explorers yet another.