Bizarro Episode: Planet of Twilight in pretty much its entirety. No matter how you approach it, this book is just plain odd.
Deader Than Disco: After Darksaber, no-one could take the "superweapon of the week" plots that had previously dominated Star Wars Expanded Universe fiction seriously anymore. In a weird way, we might have Kevin J. Anderson to thank for the subsequent new directions (eventually resulting in the Yuuzhan Vong arc) taken by the EU.
At least in the previous stories, the superweapons had already been built by competent workers. This showed us what happened when a superweapon gets built by incompetent ones.
Die for Our Ship: Callista's major fault is that she's not Mara Jade. At one point, Barbara Hambly was quoted as saying that "in Children of the Jedi, [she] was hired to write the perfect love interest for Luke, and Planet of Twilight, [she] was to write her out."
Fridge Brilliance: Bevel Lemelisk's characterization goes a long way towards explaining why Imperial superweapons are so ludicrously over-the-top: they're basically a combination of Lemelisk's wildest mental flights of fancy (the man designed WMD's for fun), married to the gargantuan resources and budget the Empire had access to. The times that he did have to cut back on resource expenditure resulted in the far more efficient (at least on paper) models like the Darksaber and the Sun Crusher.
Fridge Logic: So, Jedi like Callista can transfer their minds into computers, then into bodies that aren't their own, even if that means getting cut off from the Light Side of the Force. Why is Callista the only one who did this? Couldn't Obi-Wan have helped Luke and the Rebel Alliance more if he had, say, transferred his mind into the Death Star?