I'm not familiar with Mongoose's version, but earlier versions of traveller were never really a toolbox of generic ideas. Rather, the setting and rules went hand in hand. I think you would find that FTL travel (jumping 1-6 parsecs using LOTS of fuel, trip taking a week with no communication to normal universe), FTL communications (none), and ship weapons/defenses (missiles/particle accellerators/meson beams on the one hand, sandcasters and black/white spheres for the other) don't really fit into a Star Trek or B5 concepts. You might be able to wave some of it away with "description differences", but you might also end up building things wholesale from scratch if they are key to your ideas of a campaign.
On the other hand, the split of technology (which most space settings do) could certainly be laid out for either setting. Older technology would be easy to identify for any of those "retro" worlds that Kirk, Spock, and Bones beamed down to. Similarly, if Earthforce were barely high enough tech to use FTL (9 or maybe 10 in the classic settings IIRC), the blasted post-apocalyptic Narn homeworld may be primarily earlier tech (TL6 or 7?) for everything except weapons and presumably the Centauri would be one or a couple higher TLs than Earth (11ish?) and Minbari a couple more beyond that (14ish?).
If you're looking for a generic system, I was always partial to Alternity. They provided just enough that you could pick and choose and build a setting from. I'm sure Gurps space is good too, but I was always more overwhelmed with the amount to choose from and discarded much more than I ever used. Gurps Traveller did some of the paring down of generic Gurps Space for you, but again with the intent of casting it into the Traveller type universe/setting.
