Well I had to ask, didn't I? :P
Really this episode is just a symptom of the series as a whole. Disappointing and it could have been better. Voyager wasn't the worst of the Trek series by any shot, but it could have been the best with a bit more consistent writing and that's what made it so disappointing.
Chakotay's a great example. When I first watched Caretaker I was thinking this guy might end up being my favorite character. The aggressive, adversarial good guy who's done things the Starfleet way but found those ways wanting. Him and Janeway could have had excellent tension and drama between the two of the. The righteous Starfleet captain vs the pragmatic rebel leader.
But after Caretaker he pretty much just faded into the background and the Maquis element virtually vanished from the series. Tom Paris acts more rebellious than Torres or Chakotay. Really it just seemed they shined the light so brightly on Janeway that the only reason a first officer was even there was they needed one, but letting him do anything dramatic might take away from the captain. Really the only episodes he really stands up to her are Scorpion and Equinox. No details, but one case he only does so because she's unconscious and the other Janeway does something so insane any moral human being would have stepped in.
It's really amazing when Chakotay seems cheerful or lifelike it almost always turns out to be an alternate universe, or holodeck simulation. As I said, my theory is Janeway castrated Chakotay after he joined her crew. It's the only explanation.