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.
Author's Saving Throw: For those unhappy with Palpatine returning after his climactic death in Return of the Jedi, the Hand of Thrawn duology tosses out the idea that the Emperor featured here isn't the real deal. It's pretty easy to read this "Palpatine" as being an insane clone (or clones) with delusions of grandeur.
Broken Base: Zahn and his fans loathed this series because it brought the Emperor back from the dead. Since then the fandom of the Expanded Universe has been split in two: Zahn Fans and Veitch Fans. The fact that most other writers have sided with Zahn hasn't diminished the Veitch fans one bit.
Complete Monster: Palpatine’s cloning attempts lead to his vilest actions yet, not only by converting Luke to the dark side but also causeing havoc through the use of devastating force storms and the planet-destroying Galaxy Gun. When his last clone starts to decay, he tried to possess baby Anakin Solo and was only stopped by another Jedi's intervention that led to his final death.
Ensemble Darkhorse: The Eclipse get a much better reception than the other superweapons introduced here and of the giant Star Destroyers it's probably the most popular one besides the Executor.
Narm: Declarative statements against dramatic backdrops, bold,italics and exclamation marks all over the place.
Popularity Polynomial: At the time it came out it was extremely popular, with even George Lucas himself saying that it was his favorite Star Wars comic (and apparently remained so for several years). A decade later, it was widely regarded as absolute garbage, and admitting to liking it was seen as pretty much akin to saying that Greedo shooting first was a great idea.
So Okay, It's Average: Nowadays, while it hasn't exactly swung back to being universally beloved, it tends to be regarded as, if nothing else, a decently entertaining story that at least doesn't suffer the various issues that more recent Star Wars works tend to suffer from.
They Wasted A Perfectly Good Line Art: Dark Empire and Dark Empire II had some great line art by Cam Kennedy, but some of the coloring choices were... unusual to say the least. (Read: lots and lots of green and black.) Inverted by Empire's End where Jim Baikie replaced Kennedy; the coloring scheme was much better-thought out, but Baikie's line art wasn't really in the same league as Kennedy's work.