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.
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.