Broken Base: Less so than New Jedi Order as far as reception goes - the majority of Star Wars fans have expressed distaste with the series, while a minority enjoy it.
Character Shilling: Karen Traviss's work is accused of this by some any time her Mandalorian subplot comes up.
Designated Hero and Designated Villain: The first five books, in their Alliance vs. Corellia plotline, abandon decades of previous characterization to make previously tight-knit heroes fight each other in a stupid war. Highlights include Wedge, Han, and Leia becoming standard-bearers for the totalitarian Corellian government and Luke and Mara being 100% okay with their son joining the Alliance equivalent of the SS. It's only after they start suffering personal tragedy that they rethink their allegiances.
Ending Fatigue: The last few chapters involving Mandalore in Revelation.
Fridge Brilliance: After Jacen kills Ailyn Vel, no one in the cast — even Jacen — remembers that she tried to kill him twice in Shards of Alderaan.
Harsher in Hindsight: Back in the New Jedi Order series, Leia had a depressing vision of Jaina and herself telling Jaina’s kids about their heroic late aunt Mara. The vision seemed to have become irrelevant when Mara recovered from her illness, then 16 years later, Jacen became Darth Caedus.
Hilarious in Hindsight: When she "left" Del Rey (rumors are that she was actually let go because of her being difficult to work with, as Troy Denning and Aaron Allston have mentioned), Karen Traviss claimed that if she came back, she'd reboot the universe in order to undo The Clone Wars interpretation of the Mandalorians, as if she actually would have had the authority to do so. Several years later, Disney officially rebooted the EU, with quite a few believing it was due to this series and its sequel poisoning the EU to almost incontinuable levels.
Idiot Ball: The heroes should have been able to catch on to and short circuit the villain's plot relatively quickly. It can also apply to Jacen himself, for thinking that listening to Lumiya in the first place was a good idea.
Too Many Cooks Spoil the Soup: A possible real world version, as the series grew more chaotic, padded, and just plain weird as time went on. Notably, Karen Traviss had a widely different style of writing and concept of the universe from Aaron Allston and Troy Denning, leading to the Trapped by Mountain Lions plot below, while each author also had their own subplots and interpretations of characters, each of which would radically change the context of the series.