IMO MGT is hands down superior to CT. When I first got CT thru the reprints and tried to run a game, I found it unplayable 'out of the box'. It requires copious tweaking and house rules before it becomes playable. More to the point, many characters, created either bk1 or bk4+, were incapable of doing their jobs properly (without the ref adding 0 level skills by fiat, which is a cop out).
I've looked at MT but to me it is clunky and overcomplicated, just like bk4+ chargen, and it still over-represents military careers. Add to that it's in built task roll is ridiculous - the divisions are massive (4 steps on 2d6?), meaning that it's either 50/50, more or less autofail, or autosuccess.
What MGT does for me is present a comprehensive set of careers (only 25% military rather than 66%) and skills (and S4, CT never had the required skills - how a sci-fi game can get away without any science skills is beyond me), and a simple and robust task system that is easy to learn, plus a beautifully simple way of integrating more modern tropes like cybernetic implants and genetic augmentation. It also improves on trading somewhat and improves worldgen drastically.
The most significant thing is life and career events. I know some folk dismiss them as just fluff but they make Traveller chargen twice as good. Characters emerge fully formed, with a past, with ex-spouses and friends and rivals. This is a massive improvement. It was something always implied within a prior history but here it is iterated and integrated. Life events can offer interesting surprises too; I've had a couple of characters become psionicists halfway through chargen, which wasn't my initial intention. And connections are a good thing too; makes it easy to tie the characters into the refs setting, makes the pcs less than perfect strangers, and I like that you get skills for it too, as it allows the player a little influence on what their character is good at.
It ain't perfect. Combat is a little simplistic, but I'm in two minds over any kind of penetration rules as compared to just adding damage (unless the penetration factor is larger than the armour, penetration is identical to extra damage). The lack of lots of uneccessary tables is a bonus too. Have to wait until I see Mercenary to see if any improvements come along. But then my games aren't military in style so I'm not bothered that it's not an uber-detailed combat system.
The best thing is that is playable straight away and in one book. CT is unplayable without house rules and is scattered about several books (I have all the reprints). What's more, CT is totally unusable (or at least balanced) without doing your own chargen tables. Earlier careers don't have skills that they would have that emerge later, and many skills are totally missing. COTI is useless, as not only are half the careers military or paramilitary but the ones that aren't are wrong (ie: Rogues and Scientists - the tables will produce neither, instead you get 2 different types of technician).
As for me chargen is the most important aspect of any rpg, and most especially Traveller, then I have to say I'm pretty much satisfied with MGT, and actually very impressed by chargen itself.