have they been done before?
I just thought of a completely useless yet surprisingly cool way to arrange systems on the map: put them in a framework like the nodes of monkey bars, with jump lines as the bars. Make it fully perspectivized, so that the map appears to be a "picture" taken from a particular point in space, with the "monkey bars" getting smaller as they get farther away. I'm not sure I'm explaining this very well, so I've included 2 (very crappy) images (that I threw together in about 20 seconds using MS Paint).
From there, you could make some systems "inside" the space bounded by a given grid cube. That way, for long-distance travel, the player would tend to use the framework of what might be mostly uninhabited systems (with perhaps a refueling post now and again), but to get to specific destinations they'd have to leave the ordered grid.
...hmm, if you wanted to get really evil, you could make two seperate frameworks where the systems of one are at the centers of the empty cubes of the other, and there would be very few ways to switch which grid you're on...
Three dimensional space. That is all.