Whatever happened with that crystal gravfield trap thingy?
You know, the MacGuffin they fought a gigantic battle over in The Last Command, and it turned out they never needed it cause they already shot down all of Thrawn's cloaked asteroids? Why did they even have the battle at Bilbringi, anyways?
Mainly Thrawn's genius at work. He'd figured out that the Tangrene preparations were fake and Bilbringi was the real thing, and moved his fleet to crush the New Republic forces. Though Karrde had provided evidence that all twenty-two asteroids were down, most of the political figures on Coruscant wouldn't be convinced by just a smuggler's word - hence the Bilbringi assault was as much giving a sop to them so they'd shut up. Of course, Thrawn never counted on the smugglers being present, and he certainly didn't see Rukh until it was too late. As for the CGT...it's never mentioned again.
Also, OP, your idea of the timing is off. Karrde told them about the asteroids either not long before the raid had launched, or after. While Star Wars has never been concerned with how its Subspace Ansible works, nor whether you can receive or transmit messages while in hyperspace, it wouldn't be unrealistic to assume that, by the time High Command got word, it was too late to call everyone home.
Thrawn knew from the start that Leia is Luke Skywalker's sister. He knew that the Noghri had a near-religious awe of Darth Vader. But he still sent them after Vader's kids. That seems a little unwise, doesn't it? Shadows of the Empire has a villain not nearly as brilliant as Thrawn realizing that Darth Vader is Anakin Skywalker. Tattooine Ghost has that being common knowledge on Tattooine. If a Smug Snake could figure it out, if random people on the street knew, Thrawn would have known.
Canon Discontinuity strikes again. Or perhaps Armed With Canon. There's never been any real consensus about how many people knew that Vader was Anakin Skywalker, especially in 1991 when Zahn was writing. (Remember—Tatooine Ghost and Shadows of the Empire were written years later.) At the time, the assumption (and Fanon) was that no one knew, and the records were spotty at best (easy enough, with the Emperor centralizing power and eliminating "dissidents")—so Luke and Leia ran with it, and the official line was that Anakin Skywalker was a Jedi, but Darth Vader killed him in the purge along with all the others, and Luke and Leia were his children, who were hidden away by Obi-Wan (at the time, Owen Lars was believed to be Obi-Wan's brother) and Bail Organa respectively.
Also keep in mind that Vader gave the Noghri to Thrawn before he died. Thrawn knew that the Noghri had a serious honor-fixation, and didn't believe they'd go against their rightful lord even on the behalf of the children of their previous lord. Of course, he was wrong, and it was one of many relatively minor miscalculations that ended up adding up and bringing him down.
To add to what's said above, it's made clear that as far as Zahn thought at the time, it wasn't widely known what Vader's fate was and what happened on the Death Star: Mara was certain that her false vision that Vader and Luke both turned on the Emperor and violently killed him was true until Luke corrected her (and did not know that Vader was Luke's father until he told her on Wayland) while Karrde believed that Darth Vader was still alive and that the Empire might find and recover him one day.
It seems clear that in Zahn's tales, the events aboard the Death Star II were never made public. And in honesty, keeping it quiet seems to make more sense. I can't imagine Luke publicly announcing, "BTW, Leia and I are Vader's next of kin, so if he ever blew up your grandpa/Gundark/planet, killing us is really the only remaining way for you to take vengeance on him."
Thrawn's armor, and lack thereof
On his first visit to Wayland, Thrawn is shot with an arrow, that penetrates his uniform but bounces harmlessly off the body armor underneath. OK...but what if they'd aimed for his unprotected head? His grand plan to rule the galaxy goes right down the tubes. Surely a helmet or something couldn't have hurt.
He might've had a helmet. Zahn's writing is infamous for being sparse on details... He doesn't in the comicbook adaptation, but then again, that's the same comic where Noghri are seven feet tall and built like the Hulk.
Another issue is that nearly all training with projectile weapons is to aim for center mass. The head is a smaller target and thus harder to hit, plus has those little things like solid bone structure which would have deflected any shot that did not have a significant angle of attack on the bones, resulting in a painful, possibly even debilitating, but survivable wound. Also, Annoying Arrows to the contrary, if he had not had armor on, even a wound from an arrow in a less vital spot in the body would have been debilitating and required immediate medical attention. As for body armor and his death, Zahn pointed out that the body armor wasn't all that comfy and he didn't wear it if he didn't see a need for it. The bridge of your flagship is usually safe from personal attacks (especially by your own bodyguard). Usually...
After C'baoth takes over the Chimaera, right after they hit Coruscant (or don't hit it), why didn't Thrawn kill C'baoth? He easily could have snuck some ysalamri to an area around the mad Jedi, killed him, and cloned a more stable version (which was his plan).
If memory serves, Thrawn was planning to do just that, AFTER the battle at bilbringi, which is why it never came to pass. Thrawn believed he had more pressing concerns, like smashing the new republic fleet, and waiting didn't really impact his plans (though it might have if he'd lived, but Luke and the others would have destroyed mount tantiss if c'baoth had been there or not.
Also, C'baoth left for Wayland almost immediately after that incident, which put him safely out of Thrawn's hair for the time being; Thrawn seems to have intended to crush the New Republic first, then turn his all his attention towards his unstable ex-partner. (C'baoth, it should be noted, also seems to have been scheming to turn the clone armies against Thrawn). Basically, Thrawn had two enemies (C'baoth and New Republic), but felt that the former could wait a bit while he dealt with the latter, while C'baoth himself probably wasn't operating on any sort of timetable that would make sense to anyone but him.
Thrawn's death, specifically the attribution of the line, "But it was so artistically done," to the Grand Admiral. Why do so many readers, indeed even the comic adaption, attribute the line to Thrawn? As the paragraph reads:
"Thrawn caught his eye; and to Pellaeon's astonishment, the Grand Admiral smiled. 'But,' he whispered, 'it was so artistically done.'
The smile faded. The glow in his eyes did likewise... and Thrawn, the last Grand Admiral, was gone."
It seems clear that it's Pellaeon, not Thrawn, that says the line. Pellaeon is in shock that Thrawn was just killed by Rukh and that Thrawn just calmly dies with a smile...
It still seems a bit ambiguious to me. It's not entirely improbable that it could have been Thrawn saying the line.
I always took it as Thrawn, myself. I'd honestly never even considered, or heard it said, that it could have been Pellaeon before reading this entry. Besides, it just seems more like a Thrawn thing to say, IMO.
The statement is completely out of character for Pellaeon, but perfectly in-character for Thrawn. Not to mention that the pronoun generally describes the noun closest to it in a paragraph, which means that the "he" was describing Thrawn.
The subject of the paragraph is Thrawn. Omit the prepositional phrase 'to Pellaeon's astonishment' and no doubt of the speaker's identity remains.
Crystal gravfield trap strategy.
There are a lot of things I don't understand about the final battle for the CGT. I know what it is and why the New Republic wants it, but why exactly does the Empire have them? If Thrawn knows they're the target, why wouldn't they simply be moved? Or replaced with a decoy? Or rigged with explosives to ensure the NR doesn't obtain one? Or modified to provide false positives and ignore some (but not all) cloaked objects, adding another layer of paranoia and confusion, something we all know is right up Thrawn's alley?
By the time the attack was launched, the Republic doesn't need it anymore and are really attacking to seize some initiative from Thrawn's relentless advance. Any defenses the CGT had are irrelevant, we never see it and the Republic never tries to take it.
What happened to the Katana fleet?
It was seized by Thrawn, and used by the various cloned troops at his disposal. After his death, it and them were likely folded into the other remnants of Imperial forces throughout the galaxy.
Why did Thrawn send C'Baoth off alone with one of his best generals in The Last Command?
Okay, so Thrawn and Pellaeon clearly know C'Boath is an insane control freak who can control peoples' minds. He does it repeatedly. So why does Thrawn send him off General Covell and his best, handpicked troops, onto a ship with no ysalamiri on it? He clearly didn't plan on what happened, and yet it seemed blindingly obvious; a skill C'Baoth even uses in front of Thrawn and threatens to use again. What the hell?