MT: Characters generally CT-ish in skill levels; more levels per term, but more skills to spread them out over for non-gunbunny characters. Broader weapons skills. You can keep using HG with the MT combat system, or you can use the MT design system. LOADS of errata issues, but other than that, a solid game engine. It doesn't always feel the same as CT, and is very much "CT hybridized with Striker". But it is the most directly character compatible. Many rules poorly worded, but once understood, shines; few take the time to get to understand them.
TNE: characters convertible (sort of)... but not compatible. Combat sytem's major flaws are in damage taking. Damage system results in no lethality threat from handguns... solved often by switching to D10's for damage, rather than keeping d6's. Design system more detailed than MT, and no longer HG compatible, using neither the same ratios nor the same reuslt ratings. Really, it's Twilight2000 OTU...
T20: Characters totally incompatible with all other editions. Ship design is a variant of HG, and very close to HG. HG derivative vehicle design system, too. T&C variant of Bk2. System generation slightly revised from the CT/MT/TNE mode.
My choices of preference are MT-T20 Hybrid, MT, WODTrav, T20, CT, TNE, T4