They gave her a first officer with no personality and was little more than a yes-man for seven years. Hell, the entire series is based on Janeway making a terrible command decision and getting her crew stranded due to her own incompetence as a leader. Hell, even Troi passed the test where you have to sacrifice people for the good of the ship and rest of the crew.
That was the premise of the series, to have a ship stranded on the other side of the galaxy.
Besides, are you saying she should have sacrificed an entire world just to get her crew home? Granted it was somewhat stupid writing to have her have to make that choice, if the premise of the new show was to have a ship stranded then strand the darn thing, don't give them the choice when we all know what the outcome will be. And if they wanted that choice to haunt the crew it certainly didn't show, the few times it was brought up they pretty much just mention it in passing while making other decisions that didn't get them home either....
I do agree on Chakotay, he did basically nothing for 7 years, at least they gave Riker a few good episodes, I think the only one of Chakotay I find tolerable is the one where he meets the aliens his ancestors on earth worshiped.