It's what I loved about Benjamin Sisko in his first 3 seasons of DS9, he was flawed from the start and he had a terrible temper which could hamper plot elements but seeing him work through his own personal obstacle from an episode made him an intriguing character to watch. Janeway was in her first command and stuck in this unfortunate situation and for her it was like, "No problem, it's only Tuesday." She was so dull-witted about her situation that I couldn't buy her as a character and I agree it doesn't help her when the writers are staging every element for her to be right all of the time. I mean, a leader should have some self reflection from their actions, especially when they're bad ones. Kirk had that moment in "Balance of Terror", Picard had that in "Darmak" why can't I see a heroine, who I want to invest in, have her own personal obstacle to overcome? Shame it wasn't Janeway and it definitely ain't Michael Burhnam.
Totally agree with Sisko. The best flaws come from the best strengths. Sisko is a very bold, passionate man, especially in the captain's chair - that's both a blessing and a curse. Picard is all about reason and diplomacy - again, that can sometimes be good and sometimes be bad. Just look at their enemies. Sisko, a man of action, had to deal with the very politically minded Founders. One reason In the Pale Moonlight works so well is because that kind of action goes directly against Sisko's modus operandi. Picard, a man who always valued individual life and diplomacy, was forced to deal with the Borg, a hive mind that couldn't be reasoned with.
Janeway had... the Kazon?
I always think they should have played up Janeway's background as a science officer. She would be extremely smart and practical, but not too experienced with the military aspects of command and too intellectual to readily bond with her crew - at first, she'd be more respected than loved. Her intelligence is her strength and her weakness.
This would make a great Kirk/Bones/Spock dynamic where Tuvok appeals to Janeway's logical side and Chakotay is more of the people person, good in a fight type figure. See, the main problem with Janeway being so capable is that it doesn't leave her two senior officers with much to do from a storytelling perspective. Chakotay and Tuvok should have been the two best characters after Janeway, but they were ruined by her.