The show had such great potential,a chance to be NuBSG before NuBSG.Instead the producers were too anxious to recreate the clean cool lines of TNG that the show suffered from the curse of the reset button.Consequently you got stories and concepts that had been done so much better by other sci-fi shows not least TNG itself.
I feel sorry for poor Chakotay (and Beltran)Chakotay should have been the type of guy you would bet on in a Klingon knife fight but the character was ignored and yes somewhat castrated(metaphorically)by a very strident captain.
I think the show could have been a much better show even without trying to be 'dark and gritty'. A ship constantly on the move at high warp is naturally an episodic setup. They could have had their 'alien of the week' and kept stories light and fluffy, if they had a rich cast of recurring characters and more consistent relationships between crewmembers, and lasting damage between episodes. Continuity on ship/alien of the week off ship would have been a really good formula.