Equinox is a bad case study. Kathy's character was famously all over the shop for seven seasons, but Equinox is really the only episode where she acts like that
. So it's an easy sell for Voyager's critics to use that episode to paint her in a very bad light, but the truth is that she's fundamentally out-of-character in that two parter. Equinox isn't truly representative of who Captain Janeway really was most of the time.
I often wonder what was going through the writing team's minds when they wrote Equinox. In terms of inconsistency with the rest of the series it's up there with the dreaded Threshold. I still remember feeling "WTF?" when I first saw it because the character dynamic in that episode is just COMPLETELY off-kilter.