She was a bad Captain at times. That is on the writers, not on Mulgrew's performance which was generally very strong. I'd say who cares if she was a bad Captain? The point of the show was to be entertaining, not to show "perfect Captain Janeway". If some of her bad decisions led to more entertainment and drama then I am all for them.
Now if you want to call out the crew for not challenging some of her more questionable decisions in a stronger way that is completely fair and again that is down to inconsistent writing.
I am watching voyager again. Now in season 6, which I seen before enterprise was out. And thanks to T'pol I have somewhat became addicted to star-trek (sad because its true) and now playing X-Box STO (star trek online) and what I have seen is the whole voyager plot / casting (from the directors end) was all screwed up, I even just read that even an episode from voyager was rejected from the Star trek world.