These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Alternative Character Interpretation: There are those (in and out of universe) who feel that the Empire would have been more than capable of handling the Vong and that Palpatine had established it to deal with them, while others (again, in and out of universe) feel the Empire's track record meant the first ACI was wishful thinking.
Base Breaker: The Expanded Universe as a whole varies wildly with the fans depending on which book or writer is in question. Nothing compares with New Jedi Order on just how split the reception among the fanbase given how radical of a departure it was in tone.
Crack Pairing: Several years ago on The Force.net, Jacen X Nen Yim did a brief stint as a mildly popular pairing (often with Tahiri playing matchmaker). The two characters never meet, aren't the same species, and are on opposite sides of the war. Usually done with something of a knowing wink, though.
Complete Monster: Onimi. This is the guy who masterminded the most devastating war in Galactic History, and indirectly caused the deaths of trillions and the extinction of whole species just so that he could become a god. He even tells Jaina that he's looking forward to "exterminating everyone and everything in this foul galaxy." During his Motive Rant to a captive Jaina, he does try to cast himself as a Woobie, Destroyer of Worlds, but she rightly just thinks he's a lunatic and is repulsed. It's made clear to the reader and both Solo twins that, by the time of the Final Battle, Onimi's motivation is For the Evulzat best. Even worse, it's also strongly implied that his plan to send the galaxy into darkness had actually succeeded.
Designated Evil: The Jedi who wanted to utilize Imperial superweapons and Centerpoint Station against the Yuuzhan Vong.
Jacen: Look, one thing, no matter what we did at Dantooine, I was proud to have you at my side. I don't know what I'll be in the future, Anakin, but I know you'll be a great Jedi Knight. I have confidence that you will succeed, no matter what life throws at you.
Anakin: Are you really Jacen, or some Yuuzhan Vong in an ooglith masquer?
When the Vong send a moon crashing down on Chewbacca, killing him and the planet's population. After crossing the Horizon, they just keep going. Most memorable was their genocidal conquest of Coruscant.
What they do to Ithor. Corran Horn dueled with Shai to decide the planet's fate. If Corran won, Ithor would be spared. Corran slays Shai, but the other Vong betray him and unleash biochemical weapons that melt down Ithor's ecosystem, killing the population.
Onimi crosses this during his Motive Rant. Before, everyone thought he was just a messed-up individual. It's impossible to have any pity after learning that he knowingly caused the most devastating war in Galactic History and caused the deaths of untold trillions, and is responsible for all the pain and suffering the Vong inflict on the galaxy.
The Yuuzhan Vong. Their organic technology is bad enough, but then there's their obsession with pain and sufferin, which they consider a religious experience.
Lord Nyax. Two meters high, lobotomized to the point of no higher thought process, hunts through the Force, with six lightsabers attached to his hands, elbows, and knees respectively, prowling through the forgotten slums of Vong-ruled Coruscant searching for prey among the refugees and survivors.