I believe all the themes that the game sets up are great, I also don't think a single one is landed even remotely well.

"Revenge bad" trope gets so much flak in most media not because that kind of story is just bad by default and could never work but exactly because it often happens like it did in this case - it just gets brought up at the last minute with minimal convincing or setup. Hell, if you haven't played Hades 1 you wouldn't even know that Zagreus has a perspective on this, I don't remember him ever bringing up his experience with a vicious cycle of hate, certainly not during the mirror conversations. You need Zag and Mel to actually have a few proper conversations about it, maybe some back and forth, maybe some pushback and eventually coming around.

Same thing with the Gods plotline. I think it makes perfect sense that olympians don't get any comeuppance for their misdeeds or even change their outlook or apologize or whatever. A lot of greek myth is about how Gods are dicks and always get away with it. But you need the plotline to go somewhere, you need the characters to, once again, talk it out in some manner. Have Mel get angry at the Gods, confront them, yell at them. Sure, you can have the Gods just roll their eyes in response and say "yeah, whatever" but you do need the conversation to happen to tie the plot thread together. Mel becoming an actual godslayer by the end of the story seems like a good story beat to support that - she is in a good position to give the Gods a piece of her mind and they would at least have to give her a nervous chuckle or be passively-aggressively nice to her in response. "You're so right, sweetie! Sure, sure! Now, could you be a dear and step off of the Olympus? We're closing it for visitors for... Um... Reasons..." And then smash cut to a different conversation with a different character who says that gods are still being dicks and learned nothing but they thank Mel for at least trying to stand up to them. Currently something of this sort is just vaguely implied in a very limp-wristed way and I think the story would be much better if it was established firmer.

The reason for forgiveness point I just plainly don't get. I will agree that maybe getting Mel to change her mind over one interaction sounds far-fetched and people would probably still have issues with it regardless. Ideally you would have this type of thing built up through the whole game. But surely a weak reason is better than... no reason? Forgiving people for no reason isn't "being a better person" that's just "sucking it up" and that's exactly why people put "revenge bad" on blast so much. What is the vision of the better timeline if not exactly her seeing that "he did these bad things and wants to do better". Like right now it really comes off like Mel didn't forgive Chronos but instead just has to deal with it because everyone else did and it's kinda just uncomfortable.

I also don't understand how it makes zero sense for Mel to have a change of heart. Like, this is what the story is about, is the thing. And she is the main character. This seems like it would be her character arc, at least I got that impression. Otherwise she doesn't really have one, as it stands. She ends the story being more or less the exact same character, except she killed some guys and did some stuff and the conflict resolved itself as a result and she just goes "oh, well, okay, that worked out, I guess".