I've been reading a lot on the Legacy Era, and I generally like it. As far as gaming goes, it allows me to use the materials from all three lines (fringe characters, military characters, and Force-users) easily while having something a bit different from the standard Dark Times/Rebellion game.
That said, I still have a few concerns with it. By the timeline, the Imperial Remnant/Empire (under Fel) makes itself out to be an attractive alternative to the GFFA. In 127 ABY, tensions lead to war with the GFFA and in 128 ABY the One Sith reveal themselves as allies of Fel's Empire and help him to win the war by 130 ABY. This is where I have a mental hiccup.
The Sith are pretty well known as the historical "Big-Bad-Evil-Guy" throughout much of the galaxy. Even those that don't know much more about them know that they're bad news. This makes me wonder why the Empire would publicly acknowledge their assistance, so much that it becomes known as the Sith-Imperial War. It also makes me wonder why anyone sane would surrender to Fel's Empire when they are known to be allied with the Sith. Publicly allying with the Sith would seem to hamper the Emperor's "victory without war" policy and the goals of the Imperial Mission (both of which seemed to be sincerely pushed by Emperor Fel).
So, considering that, I was wondering if perhaps the story could be bettered by editing it to have the Sith be hidden allies of select members of the Imperial leadership (specifically not of Emperor Fel or those that will become his loyalists). The Sith would not be publicly revealed until the coup in 130 ABY when Emperor Fel is driven into exile and the Sith take control of (most of) the Empire. This means that nobody fighting in the Sith-Imperial War would have called it that at the time of the conflict, only after Darth Krayt is Emperor.
I should mention that I'm only really interested in the starting point of the Legacy Era (sometime between 130-137 ABY) and I don't have any intention of adhering to the events of the comics past that point.