Ronald D. Moore said:
We sat down and approached 'Equinox II' and tried to find what the show was about. What was the point of meeting this ship and this crew and this captain, and what did it mean? We finally landed on this idea that the two captains were going to go in opposite directions. Janeway was going to really feel the same kind of pressures and stresses that Ransom [John Savage] felt, and watch how it could turn a good, by-the-book Starfleet captain into what he had become. At the same time, his interaction with the Doctor [Robert Picardo] and Seven of Nine would rekindle his humanity. It was this nice, double track approach, but it just got lost in the translation. It has no coherence. You're not sure what's really going on. You've got some potentially good scenes. The scenes between Janeway and Chakotay had some real fire to them, and you kind of felt like she is going off the deep end, a bit. Then she relieves him of duty, and there is this crisis of command between the two of them. But at the end of the episode, it's just a shrug and a smile and off to the next.
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It has to be about something at some level. The things that Janeway does in 'Equinox' don't work, because it's not about anything. She's not really grappling with her inner demons. She's not truly under the gun and suffering to the point where you can understand the decisions that she's made. She just gets kind of cranky and bitchy. She's having a bad day; these things keep popping around on the bridge, and we just keep cutting to shots of people grabbing phaser rifles and shooting, and hitting the red alert sign, over and over again. It doesn't signify anything.
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'Two captains on different courses' at least sounds like an episode. At least there is something in it. Janeway will take something away from that experience, but not in the current version. What does she learn from that experience? I don't know how it's affected her. Chakotay, for all his trouble, he just goes back to work. There is no lingering problem with Janeway; there is no deeper issue coming to the fore.'