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.
Alternate Character Interpretation: Troy Denning's treatment of Luke Skywalker has been controversial. It was less noticeable in his previous books, but still present. Basically, Luke is The Chessmaster who plays the Sith against one another while plotting schemes within schemes. Although, in Conviction, written by a different author, Luke continues to behave this way, with Vestara saying that he's Not So Different.
Fridge Logic: After Daala gets removed from her post via a coup, Wynn has a conversation with Saba. Wynn says that Daala is "honorable". Daala, who sent Mandalorians to bully the Jedi and other people, and did not even try to moderate their monstrous behavior or punish them for it. Daala, who was cracking under pressure and was having hissy fits over the slightest mistakes. Wynn happens to have been a member of the New Republic, and he ought to have heard about Daala's actions with committing genocide. He had even seen Daala's behavior for himself. Where does he come off saying that she's honorable?
Possibly because he had the impression that despite all of her faults, Daala was doing what she felt was best for the galaxy.
He's Just Hiding: Inverted. Several fans are speculating due to the Legacy era occurring afterwards that Luke Skywalker might end up dying in this one (as Legacy has him appearing as a Force Ghost).
In Allies, the Mandalorian mercenary, Belok Rhal, ruthlessly guns down an unarmed Jedi apprentice who was only trying to negotiate.
In Vortex, Rhal's Mandalorians slaughter unarmed semi-sentients protesting against slavery. Not to mention callously gunning down the reporter who was reporting the slaughter live and in front of everyone to see.
Paranoia Fuel: An in-'verse example, as in, "Which Jedi is going to flip out next?"
The effect of Force Psychosis: everyone becomes a enemy for the victim.
You could have droches inside of you and you would never know until it's too late.
Squick: Try imagining Taalon, who is slowly turning into an Eldritch Abomination, suckling on one of Abeloth's tentacles like a puppy because unfortunately for the readers' sanity, that actually happens.
Strawman Has a Point: Daala's fears about Jedi entitlement take on a new light after the Order's decision to enact a coup in the face of other potential options to gain their rights and curtail her excess such as using mounting public disapproval and political scandals to easily impeach her.
The discussion Luke has with Daala in Outcast has Luke realize that, while Daala's security measures are rather extreme, she's also doing it so that the galaxy does not need to rely on the Jedi as galactic police, which, given the constant Jedi/Sith duels, the galaxy still reeling from the last one, is probably not that bad of an idea on its own.
The Scrappy: In-Universe, Kenth Hamner is hated by all the other Jedi.