If Janeway had originally been the First Officer and chief Science Officer (and had thus worn Science Blue for the entire series), and the original captain had been killed in the series premier and then she had to be acting captain, I don't think I would mind Janeway's horrible command style as much.

If 'Janeway is a Science Officer who had the command of an imperiled vessel thrust upon her; now she must learn the ropes of being a captain while trying to get her vessel and crew home safely' had been the basis of her character arc, then her lack of tact and horrible screw-ups would be expected--she's learning. As a Science Officer, she wouldn't be expected to be a tactful diplomat with advanced training in first contact scenarios or negotiating with a hostile party.