Legacy of the Force was the story that soured me on the EU and made me stop reading Star Wars books. The general consensus seems to agree with me that it was a bad story and a needless retread of the prequels which no one wanted.

But like the prequels, I think there were good ideas and the potential for a good story in there. Having a story where neither side is truly in the wrong and everything is morally grey could have been something truly new for Star Wars and tested the Jedi and the main characters in new ways.

The biggest change I would make would be to the awful Jacen plot which took over the story and undid all of the good ideas early on. When Luke has visions of a Sith Lord who doesn't exist, I would have that turn out to be exactly the truth. Instead of going nuts and turning truly evil, Jacen's plan would be basically the same as Lelouch's from Code Geass. After learning from Lumiya the truth about Luke's vision and seeing through the force how bad the war would get, he'd take over and unite the galaxy against him, intending to let himself be assassinated at the end to restore peace.

This approach I think would be more in character for Jacen and the more utilitarian outlook he had after the Yuuzhan Vong War than just making him another crazy Sith and would fit better with the story's early themes of a war with only innocents and no guilty.