One of the issues I have with Voyager is the sometimes dubious morals, especially with regards to Janeway.
On TNG, Picard was the undisputed moral guardian, with those memorable speeches in episodes like The Measure of a Man, First Duty and The Drumhead. DS9 had Sisko and others doing bad things, but it was still fairly clear that they were bad, even if it could be argued the ends justified the means. There was always someone like Bashir to point out the ideals.
The trouble with Voyager is that Janeway does some reprehensible things, but the episodes are sometimes written to suggest she is right. Tuvix is the classic example, almost the anti-Measure for Man. We have the ultimate irony of the hologram that has more value of life and the individual's right to choose than the captain. The episode ends too abruptly for there to be any real exploration of whether Janeway regrets her actions, or the feelings of others. What did Tuvok and Neelix make of killing a person in order to bring them back? There is that truly harrowing scene on the bridge where Tuvix pleads for his life before an impassive crew. It's done, and implied that her decision is correct.
The other one I remember is Nothing Human. It's an interesting story, in which ultimately the Doctor accepts that to use knowledge gained through horrific experimentation is wrong. Once again it's Janeway who orders the Doc to operate on B'Elanna, despite her clear wishes. At the end, Janeway has the gall to order her to forget about it. Can a captain really order someone what to think and feel? Again, it's almost accepted that she's right, and of course there is no follow-up. Torres and Janeway's relationship seems unimpaired in subsequent episodes.
There are probably other episodes in which she's presented in a far better light, or when the episode accepts she's wrong. Latent Image and Equinox are probably two. Tuvix and Nothing Human are a pair of episodes that bother me, as they seem to go against the familiar Trekkian ideals.
