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.
YMMV: The Thrawn Trilogy
Alternate Character Interpretation: Is Thrawn's continued use of the Noghri, Mara Jade, Ferrier, and C'baoth, despite it being painfully obvious they can and will disrupt his plans a case of him holding the Idiot Ball, or an indication of how unwilling he is to eliminate potentially useful people no matter how unlikely it is that they can be incorporated into his plans?
Is Thrawn's analysis of art really how he comes to his conclusions or is it simply the myth of his own invincibility that he has created?
Ensemble Dark Horse: The books produced at least three extremely popular characters - Thrawn, Mara and Talon Karrde, but the most surprising success story might be the relatively minor character of Pellaeon who would go on to much greater things.
"Funny Aneurysm" Moment: In The Last Command Han and Leia start trusting Mara after she risks her life to save their newborn children Jacen and Jaina from being kidnapped. Years later, Jacen would pull a Face-Heel Turn and kill Mara. Oddly enough the irony of this was never pointed out in the latter book.
Hilarious in Hindsight: Luuke being an insane clone of Luke Skywalker becones especially ironic when one remembers that Luke Skywalker's film actor, Mark Hamill, ends up voicing The Joker, who is an incredibly insane supervillain.
Mary Tzu: Thrawn was flanderized into this in later EU works, which led to Zahn delivering a Take That in the Hand of Thrawn duology that he was never that good. Zahn himself played with the trope in the original trilogy, as Thrawn deliberately nurtured an image of being this trope so that his enemies would lose hope, thinking everything was part of a Xanatos Gambit. The fear of Thrawn was often as much of a deciding factor in his victories as Thrawn himself.
Thrawn wasn't flanderised into a Mary Tzu. He was an extreme example of Mary Tzu right from his first appearance. Even in the original Thrawn trilogy, his omniscience is difficult to swallow. There is really little justification for most of the conclusions he reaches. Even Zahn fails to depict him as a convincing military genius, and instead he comes across as a consistently lucky guesser.
What Joruus C'baoth did to that one Imperial in The Thrawn Trilogy. We don't see it happening, but for a little while after it's over the Imperial is the viewpoint character, and he's basically nothing more than an extension of C'baoth's will. A few pages later and Captain Pellaeon sees a report that the Imperial who was escorting C'baoth just... died a few hours after being separated from the mad Jedi. Worse, Covell had already been the viewpoint character once before, and the contrast between the highly competent Deadpan Snarker that he was and the worshipful puppet he was MindRaped into was utterly horrifying.
Zahn used the Star Wars role-playing game as a mine of source material, apparently on the advice of Lucasfilm.
In the sidebar notes of the 20th Anniversary Edition, Zahn mentions a few cases where fans accused him of referencing stuff from current culture, not realizing that the references were older.
Some complained of him ripping off Star Trek when mentioning the 'borg implant' that Lando's assistant had, but 'borg' is just a abbreviation of cyborg, a term that had been around for many years before.
A reference to a Corellian Corvette (you've seen one; Princess Leia was escaping in one at the start of the original Star Wars) had some claiming he named it for the car, not realizing the car had been named after a type of small Age of Sail warship. The fact that the name for the ship predated Zahn's writing also was a factor.