I think the problem (with hindsight) was that TNE and MT introduced two different things at the same time and in the same bundle: setting and system.
If GDW/DG had introduced a revised Traveller system, then it would have received a different response. Now I think MT was a major improvement of CT, and would probably have been well received, as indeed the system was. TNE, IMHO, was a crap system and would have been received poorly.
They then could have launched the Civil War storyline, and stated that it was statted up for the new system but refs could decide. In other words, the explicit choice that GURPS Traveller made could have been made earlier.
Ditto TNE… which whilst it struck me as far too fast a collapse and recovery for an interstellar setting (just adjust the timescale of the collapse), was quite interesting when separated from the rather poor system.
I would also suggest that if you have a history in place with period of Long Nights and the “rediscovery of what was lost” as the Known Space setting for Traveller already had, then setting it in the past, or the very far future, or (as Mongoose has in the Starter Set) a very long way away, is a better option.
I liked the Civil War, and after I got over the pain of Hard Times I started to grok the idea of a post collapse and recovering Splintered Imperium… then they effed it up with TNE…