Several things, really.
Mostly it was the tools. FFS, WTH, that kind of thing. I don't generally have a problem building universes, but I do need help with the tools to build believable ships, toys, economic systems, etc. MT was my first Traveller, and building ships with it was lots of fun. Getting to build not only ships but also the weapons on it with FFS was what made it like crack for me.
The game mechanics also had a lot going for it. The core idea was that if something was twice as hard, the number of valid die results was halved. When applied to many combat tasks, this makes TONS of sense. Ship A and B are identical, but A is twice as far away as B, making it twice as hard to detect, which means you detect A on a 10 or less and B on a 5 or less. Same thing happens when you're shooting at them. Also, B will take half as much damage (assuming A is at or further than optimal range). Since the system was already in use by their other RPGs, it would have opened all three of them to combining, or at least allow players to play them all more easily.
As for the story; it wasn't too bad either. You had plenty of levels at which to start your story (part of a large polity, part of a small polity, part of a tiny polity, by your own bootstraps, as barbarians who get introduced to the galaxy in one of a dozen ways, etc) and plenty of kinds of places to explore. You could set up your own empire or take someone else's or topple someone else. You could do just about anything. The virus part was kinda annoying, but the results cannot be denied: you can do just about anything you want, from just about any starting point you want.
Most of the hate came from people who loved the Imperium and wanted to see it restored instead of leveled. Because of that, they couldn't be bothered to give the game a fair chance, and most STILL haven't. And because GDW got hit with a series of bad rolls all in a row, they collapsed before TNE could prove itself.
(Some of the hate also came from HEPlaR, which fundamentally changed the way the universe worked, but was completely glossed over in descriptions, as if they had no clue they'd just broken the whole universe with that one little change. I agree with Chadwick that ships needed a sort of endurance factor, but that wasn't the way to do it. A much less game-breaking way to do it was with a heat system not entirely dissimilar to the one used in Battletech. But, with the move toward "more realistic", I'm sure they felt they could neither do a justifiably simple and realistic heat system, nor one which didn't feel like a ripoff of BT. It's almost unheard of to find heat management in games.)