Spoiler
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I actually liked his interaction with the original C'baoth, though. Thrawn is normally very good at judging people, but he just cannot seem to handle C'baoth. He screws up with the original, first by thinking he can be reasoned with, then by underestimating the Force, and it almost costs him his life (instead, it costs him his bloodless victory). When he meets the clone, he knows not to repeat those mistakes: he's got ysalamiri to protect him from the Force, and he intends to use and manipulate C'baoth rather than try to work with him. But... he still thinks he can predict C'baoth, and ultimately he's wrong about that. C'baoth's ambition and mind control skills both move a little faster than Thrawn anticipates, and the only reason it doesn't explode spectacularly in his face is because Our Heroes intervene.
Spoiler: C'Baoth Thrawn Relations
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My reading of this book is that C'Baoth was thoroughly trounced. His ship was effectively disabled, every Jedi but Lorana was dead, and C'Baoth himself was heavily wounded. Thrawn didn't anticipate the Force choke, but that was immaterial really, the battle was lost and all it meant was instead of 'I push this button' , 'a man standing beside me pushes this button.' Not significant, especially in the face of 'I can use TF droids better than the TF, Interdictor fields better than the Vagaari, and anticipate the consequences of Force powers better than the Jedi. I knew nothing about any of these things two months ago'

Aside: One of my disappointments with TTT is that we never truly got a proper Thrawn/C'Baoth confrontation. They spent scene after scene building the tension, and then nothing happened. Might have been interesting to have Pellaeon take charge at Bilbringi (which would also show the trust and respect that was missing from their interactions) and take an ISD or two to lay siege to Mount Tantiss.