I think the problem most people have is that Janeway's acts crazy, Chakotay challenges her so she sends him to his room...then later on he's the one doing the apologizing on the bridge. Haha, this woman hardly ever has to face up to the decisions she makes or how she acts, makes it all the sadder that Bryan Fuller's proposed episode of Q saving Voyager on the brink of total assimilation if Janeway' reassesses her decisions in the previous 7 years didn't get produced.
However I do still like Equinox although I feel part I is stronger. Equinox was the episode that RD Moore got really worked up about and I can see why. Enjoyable episode nonetheless, only the Janeway craziness and the Doctor suddenly becoming like a pantomime villains just because his ethical subroutines were removed REALLY bothered me, everything else was good enough.