I like MT the brownie point system - it allows you to bank up points to get SEH's and stuff (and heretically in my game to modify dice rolls to get special duty)
I agree with Sigg (as usual) - from day one, we used the char gen system in CT/MT to develop the number of character points (a la GURPS) that a character got and then the player chose from the tables. This still left characters without edu 8+ not getting the fourth table skills (if your parents send you to a bad school, you pay the price, basically) and in Advanced Char gen it left open special duty as a random roll of the dice. Its not quite like GURPS in that you are at the mercy of what the dice give you.
Everyone I have ever played with (unless playing strictly by the rules for 'fun') has done this, so I didn't think it was all that contentious.
I play MT with additions - I have never figured out MT space combat, so I play Power Projection for that - but then I spent one whole day cutting out the errata and sticking it onto every page of the MT books to get them to work. So my investment is repayed with loyalty!
I would probably go T20 if I was starting out, because everyone these days plays 3ed D&D (or so it seems).
Although I seriously dislike it as a game myself, if you don't like D&D type rules, I would go for GURPS Traveller - you get alot of Traveller for your money and the chance to bring in other stuff from other GURPS products. (...did I really say that!, must vist the shrink...)
![Big grin :D :D](data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7)