Here are some of my thoughts after rewatching Equinox…
Janeway was so happy to meet Ransom before his crimes were revealed! He was also a Captain and a scientist and they could have been such good friends if he wasn't a mass murderer. Ah well.
If I was one of these nucleogenic aliens I would be angry at the Ankari because why would they just give the summoning device to some random aliens that they just met?
What is the long term plan of the Equinox crew when they do get back to Earth? Inter dimensional war??? These dummies desperately needed to be stopped at all costs.
The episode tries to paint Janeway as someone who is obsessed and a bit crazy because she’s (rightfully) angry at Captain Ransom and also because she tries to… enforce the Starfleet rules? Ok.
Noah Lessing isn’t being tortured by Janeway, she’s just not going to protect him on her ship (that he has endangered) if he won’t help her stop his crew from murdering more aliens. Do I think Janeway is wrong for doing this? No actually, I don't.
Chakotay thinks Janeway is being unfair towards Lessing because being loyal to your Captain is always a good thing. Ok... Then why does Chakotay openly defy his Captain's orders a few minutes later? What about the loyalty that you care so much about, Chakotay? Also, he's a former Maquis terrorist, so he should be all for putting morally bankrupt Starleet officers behind forcefields with questionable means to save innocent lives, right?
Why does everyone, including Tuvok, seem to forget that if you commit crimes towards an alien society then you get punished by that society's laws? It's literally part of the Prime Directive! We know that Janeway does not condone capitol punishment, but she knows that the aliens have every right to punish the Equinox crew. Tuvok thought B'elanna deserved her punishment in Random Thoughts, so why does he think that the Equinox crew should be exempt from nucleogenic alien justice?
This scene is cute, but honestly Janeway should not be the one apologising when Chakotay's been a rubbish first officer. Also, why does Janeway think that Chakotay would ever stage a mutiny of any sort? Has she not seen Year of Hell? Chakotay would literally never mutiny, even if it was the right thing to do...
Also, Chakotay tells Janeway that she's not just chasing Equinox to save Seven of Nine but also because she's angry at Ransom. Ok... but saving Seven is reason enough to pursue the Equinox, and also does he not know by now that Janeway would chase literally anyone who kidnapped Seven??? Does Chakotay just not give a damn about wether Seven lives or dies? I guess that's in character but... yikes!
In conclusion, I don't think Janeway did anything wrong in Equinox! Also, I love this double episode, and Star Trek Voyager in general so this is not me being a hater. Also I generally like Chakotay as a character, I just think he's a bit dumb in these episodes in spite of the writers' obvious intentions to make him the voice of reason.
I wrote a very long post about why Janeway did nothing wrong in Equinox, and then I wrote some text on pictures (I added them to the post to make it a bit less dense). This is a post with those pictures but far fewer words :)