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.
The Emperor of the One Sith, Darth Krayt was a great Jedi Knight once, but that time is long past. Seizing control of the Imperial throne, Krayt establishes a military dictatorship that violently destroys any who might be a threat. When a single Mon Calimari shipman is captured on board a rebel cruiser, Krayt flips out and kills him after ordering a summary execution of ten percent of the Mon Calimari species while the rest will be forced into camps and exterminated later. Suffering a betrayal from his most trusted follower, Krayt later returns from the death, now of the belief the galaxy must experience death as he had before launching a violent, galaxy wide campaign, with the plan to manipulate his enemies to use a toxin against Coruscant, the most populated planet in the galaxy, that will kill everything on the world except the Sith.
Vul Isen is a Mad Scientist whose job is genocide. When Darth Krayt decides the Mon Calamari species needs to die, Isen is appointed as the one to expedite the process. Isen's first plan is to create a sea monster known as a Leviathan that steals the souls of its victims and imprisons them in eternal anguish. When this is destroyed, Isen develops a toxin to kill all life on the planet. Despite the best efforts of the galaxy, Isen exterminates 80 percent of life on Mon Calamari with nothing more than satisfaction at his own brilliance. He then proceeds to attempt to exterminate all life on another planet that defies the Sith after having refugees hunted down
The Imperial Knights in general have proven very popular, with Hasbro making figures of Krieg and Draco, a rare honor for Star Wars characters who have never appeared in any movies or tv series. The author himself credits the knights as the most popular part of the comic.
Evil Is Cool: Pretty much all of the Sith, but especially Darth Krayt and Darth Wyrrlok.
Evil Is Sexy: Darth Talon seems to have been designed to invoke this.
Family-Unfriendly Aesop: If the Galactic Alliance and Jedi had thrown the (innocent) Yuuzhan Vong under the bus, its order of battle would not have been fractured and it would have won the Sith-Imperial war.
Darth Krayt's immediate destruction of 1/10th of the Mon Calamari and slow genocide of the rest via forced labor proved that despite his nice rhetoric, he's as nasty as any other Sith when pushed.
Vul Isen crosses it when he wipes out 80% of the population of Dac. Not to mention his poisoning of Da Soocha for harboring Mon Cal refugees.
Roan Fel may have very well crossed it. He decided to have Darth Maladi create the Alpha Red (actually Omega Red) bio-weapon so he can use it on Coruscant. In exchange, he has her released so she can try to kill Cade.
They Changed It, Now It Sucks: Some had this reaction to Luke being dead. Never mind the fact that it's perfectly reasonable: the series is set well over a century after the OT and Luke died of old age.