Traveller: New Era (TNE) is reputed to be a controversial version of Traveller; from what I've heard, when this game was released back in 1993, it split the fan-base, as not all players were content with the significant changes in the setting, not to mention a new and different ruleset (the GDW "house system" also used in Twilight: 2000). Indeed, much criticism has been leveled at the Virus - a self-replicating cyber/bio weapon capable of taking over most computerized system and the reason for the TNE post-apocalyptic condition, as well as at the departure from the "Golden Era" milieu of Traveller (or its Rebellion extension). In this post, I will avoid the subject of the Virus for the most part, though I will mention some of its impact on the setting. Instead, I intend to talk about a few key elements of the New Era setting, which I consider to be very good for the game, especially for a sandbox game, regardless of the ruleset (which I do not care much for).
The first is the removal of the over-powerful overbearing interstellar government (Imperium) of late Classic Traveller and of Megatraveller. While the Imperium, indeed, is a well-loved setting among many fans, it does have its limitations, especially in its "modern" form - a very powerful, omnipresent government holding multiple multi-kton battleships in every subsector. This (the "Golden Era" and the Rebellion) is a setting where many elements are far beyond the reach and influence of players, and players typically are pretty low on the political foodchain. The "endgame" elements of a sandbox - that is, influencing planetary and interstellar politics and maybe even establishing a pocket-empire ruled by the PCs - are very difficult to pull off with interstellar "big government" and big corporations running around. TNE removes them, albeit in a very brutal and total way, but suddenly there are much less "big boys" running around and either foiling the PCs plans, or making them redundant. Less authority figures around is a good thing for a sandbox, as it makes the PCs important, and makes their decisions meaningful. Even when governments ARE involved, they are much smaller affairs than, say, the Megatraveller factions, and thus much more amenable to PC influence.
The second, and related point is the opening up of a real frontier for actual exploration. A recurring problem with the "Golden Era" was that, unless you used semi-canonical peripheral regions such as the Outer Rim Void of A4: Leviathan fame, there wasn't a "hard" frontier to be found. Sure the Spinward Marches were a relative frontier, but they were fully explored and fully known, all a developed, or semi-developed, part of an existing interstellar empire. TNE wiped the map clean, and now whatever polity the PCs are part of (say, the Reformation Coalition) has a "hard" frontier around it, and, beyond it, vast tracts of space which is either unexplored for 70 years, or very minimally explored. So you can boldly go where no man has gone before.
The third is having an actual framework for adventure. The PCs are, by default, Space Vikings - government-sponsored explorers, raiders and privateers out to explore, and loot, the Wilds. This is somewhat akin to the "dungeon crawling" of old-school D&D - PCs are out there to recover treasure, make a name for themselves, and, eventually, topple tyrants and leave their mark on the setting. This also allows for "treasure" - high-TL goods recovered from dead 'boneyard' worlds and from regressed colonies. In a sandbox, this is very useful - PCs have a motivation to take risks, to explore, and to interact with the setting and with its factions, and it is also very easy to explain why a very diverse group of PCs work together on one starship (they are all out to get rich from off-world plunder). this becomes even better with a built-in patron for the PCs - the Reformation Coalition Exploration Service (RCES), who may provide adventure hooks and assistance, all while being unable to have a significant level of control over the PCs during the adventure itself (resources are limited, and, outside of the Coalition itself, interstellar government, or even significant RCES oversight, are very rare).
With the three elements above, TNE allows for many sandbox gaming possibilities, for exploration and for meaningful PC influence on the setting, all of which are very good things.
(Last but not least, on a side-note, TNE finally gave us a reason why Traveller computers, robotics and cybernetics were limited in scope and very bulky (other than the game being published in 1977, that is) - the reason given in the new (2000's) Battlestar Galactica. In other words, people deliberately opt for very primitive electronics to keep Virus infection risks at a bearable minimum.)