[*]have Chakotay question her decisions so often
Because one of them is a Starfleet captain who follows regulations, and the other is a Maquis rebel. It would say more about Janeway if they DIDN'T fight occasionally. Also, it gave the writers something to do with Chakotay other than dance around a fire on the bridge.
[*]have Seven question her decisions so often
Because Seven was an ex-Borg drone who was completely unaccustomed to the way humans operate. Most of their conflict was about human nature, and there were many times that on the surface Seven mistook Janeway's comments as hypocritical. This hardly happened at all during the later seasons because Seven came to appreciate Janeway's push.
[*]have the doctor keep a record of her dubious decisions
He's a perfect hologram who spends all day in sick bay and has no experience at commanding a ship. Who is he to judge Janeway in that field? And it was clearly a passing joke, and not a serious allegation about her command ability. A comment like this could only have come from the Doctor.
[*]have other crew members criticise her
To create conflict and discussion. Often their criticisms lead to Janeway changing her outlook and giving them the benefit of the doubt. I can think of many times that the crew disagreed with her, and she'd go with their idea.
[*]make voyager her first command
Because it feels better when they're a virgin. Nobody likes sloppy seconds.
[*]Have arterius point out that she was responsible for his homeworlds destruction
See below
[*]Have species 8472 point out that she helped the Borg to murder them
Because she indirectly did. She made a mistake. Showing her make a mistake doesn't mean she being portrayed as an idiot captain. It meant she was portrayed as a real person who makes mistakes and has to face the consequences of those actions the best she can. It doesn't mean she was intentionally written as a bad captain. But it means she wasn't portrayed as unbelievably perfect to the point of being a crappy pretentious character.
[*]Have Tuvok say Janeways methods are unorthodox (it is her greatest strength as a leader but unfortunately, it is also her greatest weakness)
He's a Vulcan. He refers to her methods as unorthodox because all humans are weird relative to Vulcans. Vulcans think smiling is unorthodox. This is why they made an interesting pairing on the show. He also couldn't improvise, tap dance, or drop a phat beat very well. These would all be unorthodox.
[*]Have the crew combine forces in "night" to stop her "being erratic" again and refusing to follow her emotionally compromised orders
They did an episode about 4 years of commanding her crew through the DQ catching up to her. They also did an episode about Be'lanna trying to commit suicide. Gonna start a vendetta against her too for being unstable and suicidal? I don't think she made any bad command decisions in Night.
[*]Have her lose the plot in "equinox" and start attempting to murder a man and when Chakotay stops her, she's says nothing and just walks off like a sulking child
There is a deleted scene that explains that a time dilation bubble in her uterus caused 5 years of PMS to simultaneously afflict her. But they realized they already did an episode where a time dilation bubble in Chakotay's brain caused his charisma to get lost in the future, so they decided to delete the scene.
[*]have admiral Janeway say "i forgot how self-righteous i used to be"
To show that these are two different Janeways. The Janeway from the future wasn't exactly following protocols, and the differences were supposed to highlight that future Janeway had turned out a little worse than ours. It's all relative. Sure, she got the crew home, but remember that she broke the Prime Directive and the Temporal Prime Directive in so many ways to do it.