The death of Anakin Solo. Invalidated Chewie's sacrifice
The death of Jacen Solo and the whole prequel retread Darth Caedus thing.
The death of Mara Jade Skywalker at Jacen Solo's hands.
I admit i kind of like Kotor II not as good as part one but i hated that it introduced that every Sith has to have a double bladed lightsaber like Maul, whom Lucas stole the idea from Veitch or Anderson cannot remember whose idea it was for Exar-Kun to have a double bladed weapon but it was not red.
Surprised the reprints and digital version did not have it recolored to red.