Creator Backlash: Timothy Zahn has said in an interview with Jedi Council that he wasn't happy when he found out that Mara Jade was getting killed off, feeling that there was more that could've been done for her. The interviewer also asked him about how he felt about Pellaeon's death, though Zahn focused more on Mara, so whatever he feels about Pellaeon, though suggests that he's more concerned about how Mara died.
Franchise Killer: The negative reception for the series has stopped any potential post-New Jedi Order stories from being made, aside from the Fate Of The Jedi series that is considered to be an Author's Saving Throw.
While the Expanded Universe was always iffy on if it was in terms of continuity with the movies and The Clone Wars, it was pretty much accepted that they still took place in the same universe, with elements from the novels being incorporated into the show and movies. Legacy of the Force was so poorly done that it might just be one of the leading causes for the EU getting rebooted when the Disney era came around.
Official Fan-Submitted Content: Readers voted in a poll to choose Darth Caedus's Sith name, with the others being Darth Acheron, Darth Judicar, Darth Paxis, and Darth Taral.
Troubled Production: The series ran into this due to growing animosity between the authors. Karen Traviss was well known for a series of side stories at the time that she had worked on exclusively and thus was never part of a rotating series like Troy Denning and Aaron Allston had been. She was also notorious for never reading other people's works within the franchise, often causing huge Continuity Snarls within a franchise that tried hard to keep things consistent. She was also difficult to work with, as Allston once mentioned how he had wanted to tie the Mandalorians into Fury better, but Traviss outright refused to divulge her plans for them to him. Denning also made various snipes at her as a result and outright ignored much of Revelations when it came time to write Invincible. Traviss had also suggested various unpopular decisions like Mara's death and never bothered consulting the other writers about if they had plans for the characters, an act that is considered very unprofessional to other SW writers at best and downright insulting at worse. Given this bad blood, it's no wonder the series ended up how it did.
Unintentional Period Piece: Released in 2006, this series owes a lot, thematically, to the War on Terror, what with Jacen ranting against his parents' support of a totalitarian government and the terrorists that work for them (which is true), while his family is dismayed at his curtailing of democracy and personal liberties in his struggle to defeat them (also true). In general, tastes-like-dirt cynicism that imbues the work is pretty emblematic of the American zeitgeist in 2007, and it's something that the series has consciously avoided ever since.