This is actually split into two concerns:
1) Some mods may need to have things that are the same faction as the player (for example, for friendlyFire station flag disabling reasons) - these all show up as white, just like the player ship dot itself. This sort of works, sort of doesnt.
2) Wingmen, autons, and other allied followers all show up as a plain green, it would be nice to be able to keep track of them with their own color. Might also be useful to be able to set a station as allied for mod/UI purposes so its distinct.
As a historical note, Escape Velocity used color to distinguish allied and neutral ships. It also used color to indicate accessibility for stations and planets: one feature EV had that Transcendence doesn't have is that there was a distinct color (orange) used for planets and stations that were non-hostile but restricted landing, similar to Black Market and Commonwealth Fleet stations before you have the appropriate ID.
Color radar required a special IFF decoder item to be installed on your ship, otherwise the radar display was monochrome.
Ship size was also distinguished on radar if you had a "density scanner" item installed. This was handy for, e.g., telling fighters apart from capital ships at a glance.
I like wtdn's suggestion.