Dear god Eve's map in 3D... yeah no. Thanks, but no.
Besides, once you start traveling from star to star in discreet fashion, the angle/attitude to that star stops mattering because...
Wormholes wouldn't follow a 3D map (two points in space, anywhere in space)
Hyperspace wouldn't follow a 3D map (it would, in fact, be an x+1th dimension - in this case, a 4th)
Jump drives wouldn't follow a 3D map (they travel any distance within a maximum, the attitude is irrelevant)
...was there another FLT method?
Again, 3D only matters once you are in the local system, and really it just greatly multiplies the number of acceptable approach vectors (so fortifications on pluto are useless if the enemy attacks from "above" mercury). So the game would not be "totally different" it would be exactly the same, except you could enter the plane ecliptic at any point instead of only the borders.
Makes sense.