I'm not fond of the way the Great Sith War was ultimately handled in the pages of the TOTJ storyline The Sith War.
Prior references to the war in other comics and books built the Sith War up to be this huge, galaxy-spanning war between the forces of light and darkness that spanned several years and brought the Jedi close to the brink of destruction. But when it was finally depicted, the war lasted all but under a year and consisted of a few battles in a few systems.
KJA was the writer, though, so it all makes sense; he's good at taking other peoples' ideas and sucking all the grandeur out of them.