Agreed on the C/7 front; that relationship makes about as much sense as a shark growing wings and flying to Europa.
In terms of chemistry, I always thought that Janeway and Chakotay had some very real chemistry, they simply could not act on any of those feeling being in a command structure. From my perspective I've always viewed it as a very deep emotional friendship/relationship.
The only episode I saw evidence of the deep emotional friendship/relationship, was that season 7 episode... oh I forgot it's name... Fractured or something like that? Where the ship was trapped in some sort of time anomaly where different parts of the ship where in different times. Chakotay had to take season 1 Janeway through the ship and explained all this in past tense.
As I said, I never really saw Janeway ever regard Chakotay as an equal, just as a yes-man. Certainly she never really listened to his advice all that often. If she had a moral crisis she either went to Tuvok or just pulled an "I'm the Captain, I'm making the call" moment.
Yeah, the episode "Shattered" in season 7 is another instance of that IMO. I've never really seen as much inequality between them as you do, but I do agree that far too often Janeway used the ole "Captain's Prerogative" to get her way, and that way was not always the right one.
And yeah, Chakotay's "Angry Warrior" speech wasn't him surrendering his manhood. (I'd joke this had long since already happened.) It was just another Native American cliche veiling that he wanted them to stop focusing on what they lost and build a life on planet nowhere together.
Meh...I don't think he ever really gave up his manhood, but was certainly dimished by poor writing.

The Doctor and Seven both stood up to Janeway to be certain. But by season 5, Voyager was TOS like in it's "Big Three" being Janeway, Seven and the Doctor, so they could get away with this. Not like either of them were insecure about their positions on the ship anyways or wanted to advance anywhere. What's she going to do? Demote them?
Paris seemed to get away with a lot in regards to Janeway. For some reason she regarded him affectionately. All kinds of speculation on why this is, be it she's his "pet project" to reform, that he rocked her world in Threshold, or plain old nepotism since she's buddies with his daddy(this gets my vote). Thirty Days was something she really couldn't overlook if she wanted to maintain discipline on her ship, since he did basically openly defy her and her orders. Even so, he got his rank back real quick.
Kim? He was quite literally Janeway's whipping boy. I swear, she just like messing with him at times. Sure he stood up to her in the Disease, but he was under the influence of the alien STD in that one. Otherwise he never would have had the spine to do that. And I can't think of -any- other situation where Kim defied her. Kim did once angrily voice objection to Captain Tuvok in Resolutions, but I'd dismiss that as a need to get back to his one true mistress.![]()
Poor Kim... when Voyager left Earth Nog was a janitor at Quark's, and that janitor made lieutenant before him.![]()
Seven and the Doc weren't ranked, so really she couldn't do that much aside from confinement (which she did with both Seven and the Doc on seperate occasions). Although they did not get away with things, namely Seven's disobedience in "Prey" and the Doctor's compliance with the aliens in "Renaissance Man".
Paris definitely did get away with a few things and seemed to be the Voyager funny-man. "Pet project" seems reasonable, although nepotism is more logical. I'm certainly more partial to those than the idea that he "rocked her world in "Threshold."" (

And on the subject of poor Harry, yes he was Janeway's "whipping boy" as you put it. She was messing with him at times (what was all that in "Twisted" about him being "one of the bright parts of the mission"?

Being an Ensign for seven years was ridiculous; he should have been promoted halfway through the series.