Well one benefit the modern ruls have is in the basic class/career choice. I think this is superior to the straight classes for a variety of reasons. The best one is that it allows diversity to careers. One can do a lot of different things in the service-some people my be smart, others fast, and others tough- A naval intelligence officer looks very different on paper than a veteran spacer maste chief who has been thrown out of every bar in five subsectors.
Similarly a marine interrogator might look very different on paper than a marine grunt.
Having marines as an occupation rather than a class opens the door to a background generation system more in line with the LLBB's.
Secondly, T20's prestige classes are shite, for the most part. A change to D20 modern opens the door up to a more diverse range of prestige and advance classes.
Yet somethings should not be changed: the stamina/lifeblood system is subtley different from the massive damage system. The armour rules in T20 produce interesting results, and see to capture some of the deadliness of original traveller combat.
Also the base attack values in T20 modern are too high for most classes, traveller is meant to reflect that trained personnell will be vastly superior at combat than untrained.
I guess I seek to have a system as diverse as GURPS Traveller in terms of character possibilites, yet that is as easy to run as T20. This could be the way to a happy medium.
I would also think about the spycraft system of complex challenges invovling long term skill use.
I agree about the starship combat system needs development, but really that is something that should be handdled in its own supplement.