I think a major problem with how Captain Janeway was written, was that she was written as "the woman captain", instead of a captain who happens to be a woman.
It seems like because Janeway was a woman, no one could really challenge her authority and the crew had to fawn over her. Chakotay, despite being a rebellious terrorist commander, seemed far to willing to defer to Janeway then he should have. Torres, another former terrorist, seemed to begin worshiping Janeway right away. Heck you think the former Maquis members would have unhappy with Janeway with stranding them there in the first place, but no, that wasn't the case. Plus Janeway seemed brook almost no dissent, Picard and Kirk were not so fragile that couldn't take a little criticism or different opinions. When Picard was replaced by aliens and the impostor Picard did reckless things, he was relived of command, that never seems to happen when Janeway does something reckless.
I think Ben Sisko came off more as a captain who happens to be black, rather then the "black captain". Sure Sisko's race played a part in a few episodes, but the writers didn't try to turn him into a Mary Sue, because of background.