From what I've read, MT was supposed to be 'classic version 2' with a lot of scattered rules gathered and cleaned up and a task system with difficulty levels introduced instead of all the various mods from classic.
I hadn't played classic, so I can't speak to which was better, but that was the main thrust of the designer's notes. The MT system works fine, we ran games with it, there were bits that people could quibble with if they wanted, but find a system without those.
The Rebellion itself - again, from the designer's notes, it seemed to be an attempt to let PC groups do heroic deeds of derring-do. The difference was, instead of a bank job in 'the Imperium' that would make them hunted by police all across Strephon's Imperium, you could pop across into enemy territory, do your derring, and be home in time for cornflakes.
But.
Lots of implausible stuff happens, because it was 'in the script'.
Most of the scripted events were of the un-fun variety, frankly. MT's 3I was set up as a place for the PCs to save the day, but they trashed the whole Imperium to do this. Worse, almost the only material released were the core books, telling you what the latest nastiness was. And no faction was winning, so everything just ground down.
I think there was some staff turnover at one point, and there actually were some adventure materials done later in the period - Astrogator's Guide to Diaspora, Arrival Vengeace, Assignment Vigiliante. Those were all good, but not worth trashing the Imperium for. But by then, the horse was out of the barn.
Eventually the company called it a day, got out the broom that was Virus, and swept the whole mess into the New Era so they could try to pick up the pieces. TNE got blamed for 'ruining Traveller' but I think the Rebellion really broke things. I mean really, the Emperor and his family are assassinated but the assassin fouls up so badly he has to flee - what good is going to come from that start?
The Imperium was big enough that it could offer anything a group of PCs could want. Yes, if they decide to be bad guys, they're going to get chased.
So, no, I did not like the Rebellion timeline. The above products were good, I enjoyed the COACC book a lot, the Referee's Companion has lots of good background info. There was a lot of though-provoking commentary in later "Traveller News Service" updates in Challenge magazine. There's a lot there that could do you well in any Imperial campaign.
I *do* recommend MT for its character generation, though - I'd suggest that if you want 2d6, use MT rules. Or if you want d20, use TNE rules, also good chargen rules. But for the sake of the tens of billions of innocent Imperial victims, don't play Rebellion background.