There isn't any mapping from 3D to 2D that will preserve pairwise distances between all points. Using time as a measure doesn't fundamentally change anything about the problem, since instead of "distance" being measured in km/AU/lightyears, it's instead measured in hours/days/years - but you still just have a series of pairwise distances between points.
You could make a locally oriented map that accurately shows distances from your current location (A) to any other location (B or C). But this type of 2D map would not accurately represent the distance between B and C.
Because you cannot map directly from 3D to 2D and preserve distances, a subway-style abstraction might actually be just what you need. You simply label the subway "legs" with the true 3D distance between points, since you cannot measure the legs on the 2D subway map and get an accurate value. 204
One just needs to be aware that there will be distances that are not reflected in the visual representation of the subway map - some points that appear close together might actually be far apart, and some points that appear far apart might actually be close together.
Note that this distortion is exactly the point of a subway map - it purposefully distorts distances in order to have a more visually pleasing layout. There's no reason you couldn't draw a map of the London Tube that perfectly represents the pairwise distances between all stations (it would just be a regular map), but that is antithetical to the whole impetus for the subway map in the first place. For the star map, you can't perfectly represent the distance in 2D, but you can still try to organize it in a way that minimizes distortions.
It's the job of the mapmaker to choose the representation to minimize that visual disparity, and to put those visually discordant distances in less important or less traveled legs. You can take advantage of natural "projection planes" to minimize distortions, leveraging the knowledge that galaxies and solar systems tend to be much wider than they are thick - projecting a galaxy top-down along its axis of rotation will only lose a fraction of that pairwise distance information (the projection distance is a good approximation of the 3D distance). An edge-on projection, on the other hand, would lose a great deal of that information. 204