That was one of the many reasons I loved the Thrawn trilogy--it showed that the fight against the Empire did not end with the Battle of Endor, and that the Rebels had spent the next five years trying to take back the galaxy from the remainder of the Imperial fleet. It was a long and difficult series of battles even before Grand Admiral Thrawn returned to rally the Empire, and of course setting up the "New Republic" was an even more difficult process of slow diplomacy, trying to convince the galaxy one planet at a time that a viable new form of interstellar government could be established. And all the while the Rebels were strapped for cash and subject to divisive political infighting. To my mind, this was an extremely realistic portrayal of what the state of things would be after such massive upheaval; though of course in true Star Wars fashion most of the focus and problem-solving lies with the heroes doing what they do best.

To me, the Thrawn trilogy in effect is the sequel trilogy, episodes 7, 8, and 9 in written form if you will. I wouldn't want anything to replace that for the world. Episodes 1, 2, and 3 have yet to be told to my view, and most likely never will be, because doing so would require throwing out the official prequels and starting from scratch in a way that will mesh with the unaltered original films.

Editing to add: Bingowings' post above is spot on.