Why Wasn't Neelix considered a candidate for removal after season 3?

[Prax]

You're right, their closeness on Voyager was partially due to their friendship of 20 years but it didn't prevent Janeway & Tuvok from having disagreements from time to time. But contrary to Chakotay who was rather "brutal" in his opposition not systematic but regular (honestly, if his Maquis crew had been larger, I'm pretty sure that Chakotay wouldn't have hesitated to throw a mutiny), Tuvok knew how to confront her friend with her contradictions and/or to advise her without antagonizing her in her cuttings off. -> I'd say that Tuvok was the voice of reason of Janeway and because of that, she listened to him more closely (besides, even Chakotay recognized Tuvok's great influence on Janeway and we saw that when Tuvok was in bad posture, he turned irrevocably to Janeway for a physical, moral or intellectual support -> they understand as nobody and that's what is great.



If I remember well, Chakotay's disagreement with Janeway were often due to what they were: Janeway thought as a Starfleet commanding officer while Chakotay thought as a Maquis commanding officer (although, himself a former Starfleet officer but I guess that since, he rejected Starfleet's policy & rules) and althought he wore the Starfleet unifom, he didn't stop thinking and acting as a Maquis throughout the journey (he was lucky that Janeway let him acting like that!). Result: 1 given situation, 2 points of view diametrically opposite to respond (and same thing for the tools used, of course).
-> whether it was Cuvit or Tuvok, the disagreements with Janeway would have settled in Starfleet style : cf Kirk/Spock; Picard/Riker : no direct confrontation. the XO suggest without trying to impose his will, what Chakotay tried too often to make a passage in force with inconvenient results.
-> if Chakotay was angry with Janeway's behaviour in Equinox, I wonder how he would have react with Sisko, who, when he had an objectivein mind, went to the end and no matter the consequences. Both would certainly have come to hands to resolve the conflicting situation and it isn't sure that the winner would have been Chakotay, in spite of his experience of boxer.

Chakotay's big disagreements with Janeway were when she was acting contrary to Starfleet Values.

-She wants to take sides in War. The side she chooses is the Borg! Chakotay objects, because he shares Starfleets values. He was a career officer, and even as a Maquis, he is still a Federation citizen.

-Janeway has a Vendetta with Ransom. Chakotay doesn't like it. Janeway later attempts to torture(or threaten torture) one of Ransom's crew. For Chakotay, Janeway has completely crossed the line. He takes matters into his own hands. Janeway relieves him, but later admits she was wrong.

I can't see Chakotay ever supporting a guy like Eddington, who used his position at Starfleet dishonorably. Chakotay resigned peacefully (as far as we know) to go to the defense of his friends and neighbors, since Starfleet couldn't interfere.

And Sisko too. Chakotay would be disgusted by what he did during his own irrational vendetta.

 

[Tenacity]

Maybe transfer her to security/tactical, the post vacated by Tuvok after becoming the first officer

BeLanna is a trained Engineer, there's no evidence that she knows the first thing about tactics or security. She would be a complete amateur.

If Tuvok became first officer, it would make more sense that one of Tuvok's senior subordinates replaced him. Someone specifically trained in that specialty.

Wesley didn't outrank laforge because laforge was the chief engineer.

Wesley didn't outrank LaForge, because LaForge held a higher rank.

If Wesley held a higher rank and wasn't a department head, he would outrank LaForge regardless that LaForge was a department head.

 

[Ghislaine H. B. BRAEME]

Chakotay's big disagreements with Janeway were when she was acting contrary to Starfleet Values.

So, Chakotay is the good guy and all Starfleet people are the bad ones... Sorry but I disagree with you. Both made some discutable debatable choices: some worked and some others didn't.

-She wants to take sides in War. The side she chooses is the Borg! Chakotay objects, because he shares Starfleets values. He was a career officer, and even as a Maquis, he is still a Federation citizen.

She didn't take sides but made a tactical choice in accepting to help Borgs, to save her people in the face of one of species the most dangerous living in DQ, which would not have missed to attack Voyager after having ended it with Borgs. Yes, it was risked but it eventually ended well eventually. And, it was not so different of Chakotay's plan to in Alliances, to make an alliance with the untrustworthy and violent Kazon. But in this case, it didn't work well.

-Janeway has a Vendetta with Ransom. Chakotay doesn't like it. Janeway later attempts to torture(or threaten torture) one of Ransom's crew. For Chakotay, Janeway has completely crossed the line. He takes matters into his own hands. Janeway relieves him, but later admits she was wrong.

So, what shoud she have made? Let Ransom and his crew leave with the equipment and abandon Seven and the Doctor to their fate? Maybe her reaction was extreme but not only Ransom betrayed her trust but he and his henchmen attacked the crew - and we know how much she is protective of her people -, but not getting back the equipement stolen as well as Seven/EMH was an assured condemnation to stay and die in DQ. Thus it was a question of survival to find Equinox and Ransom. On the other hand, I remember that Chakotay reacted in a irresponsible way in Manoeuvers, when he stole a shuttle to face Seska - for a hurt ego-, depriving Voyager of an additional means of transportation and forcing Janeway and her crew to put themselves in danger to go to get back him.
As for the torture threaten, it was maybe extreme but required in my opinion. It allowed to save Seven of a hideous death. Noah Lessing would have been able to stop everything if he had accepted to speak but instead of that, he defied her strongly to the point that she could not make differently, especially as the time was in a hurry.
The question is that would have made Chakotay in the same position? According to me, he would have used his fists to make Lessing speak (more acceptable than (an attack of these tiny creatures?) or he would have been ready to sacrifice 2 crew members!

And Sisko too. Chakotay would be disgusted by what he did during his own irrational vendetta.

Yeah, what a chance for Chakotay to have fallen on Janeway - who was more than correct with him during this journey of 7 year! - and not Sisko. He would be dead or imprisoned somewhere in DQ. In any case, even free, Chakotay would certainly not have benefited from such a room for maneuver!