I liked Tom's role in this. He really was the hero of the episode. Though the Kazon demonstrate how stupid they are yet again. Their idea of a prison is a room you're told not to leave? That has a working computer with sensitive information? Those morons deserve to lose. How do they even keep those ships they stole working? I can just see a dozen Kazon with "Warp Engineering for Dummies" books fumbling over a warp core.
As for Paris/Chakotay, for awhile I was actually thinking they remembered that Paris and Chakotay didn't like each other as painfully established in the pilot, during this arc. But it was a false alarm of course. No more friction and the reset button was applied.
Neelix brushing the Doctor aside was beautiful. Picardo always delivers a top notch performance and his wounded ego cannot be denied!