Janeway was a bad Captain because the writers tried to make her a strong woman. And that never pays off. Same thing happened with Judi Dench's M in the new Bond films. Or President Roslin in nuBSG. They want them to appear strong and determined, and somehow that means that they make bad, morally questionable, controversial decisions. As long as they are tough while making those decision, it's fine.
Janeway is wrong so many times during the show it's not even funny anymore. She sticks to her wrong decisions until almost everyone disagreed with her and tried to talk sense into her.
I disagree about Roslin, I thought she was an extremely well written character. The only really bad decision she made was not stealing the election from Baltar.
But yeah, most screenwriters tend to think 'Strong woman' means either 'A man with boobs' or 'A woman who provokes people arbitrarily'.
In the case of Janeway her wrong decisions tend to all carry the same theme: "We must get home at all costs, but we must also not defy our principles". And that was written into the character so early the writers could not have ignored it.
And whatever problems Janeway had, she was way better than Archer. At least Janeway had ways of expressing herself besides tilting her head slightly, crunching her nose a little and acting indignant.