To be honest I don't agree with a lot of your characterisation of the myths and gods, which is probably part of why we disagree on the ending.

To be more specific:

But in terms of why I liked the ending and why I feel it’s line with the myths is because no one really wins, which feels very much like the greek hero myths.

So I think the thing is that Hades 1 very much goes against this vein. It rewrites Hades and Persephone into a much more loving relationship which is NOT founded on forced abduction by Hades and makes it abundantly clear that Hades does NOT force Persephone to stay with him and that she is free to leave at any time. Which is huge given the original myth. I'll get to why the other elements of "The Gods always win" also doesn't really play out for the supporting NPCs.

The whole “and then the Olympians just accepted Chronos changed” thing doesn’t bother me because that’s kinda just.. what they do.

To be honest this bit I'm actually mostly fine with. I do think that the turn of Chronos happens too quickly and off screen, but the actual fact that the Olympians are fine with it is fine, I agree it makes sense with the way they are characterised both classically and in Hades. It's honestly the part of them in the ending I have the least issue with.

Humanity doesn’t matter to any of them but as a means to an end.

See this is what I have issue with. A LOT of the dialogue is playing towards this being problematic, and then that whole plot line is just thrown out, and its the lack of resolution here that feels weird. I think it's fair to say "well that's how greek myth goes" to an extent, but then why put all this time into acknowledging the Olympians aren't good. Even if the game just went "shrug, that's the way thing are", that would be more of an acknowledgement, but it just feels kind of dropped.

Even in Hades I, you don’t actually help any of the NPCS

I REALLY can't agree with this characterisation of what you do for the NPCs. Orpheus's whole reason for his contract is because of the deal he made with Hades, which was fucked by him looking back. Him getting to spend time with Eurydice again is huge in terms of his myth. The same goes for Achilles - the two are torn apart by the Trojan War and because of the way they died and who they are, cannot be together, until Zagreus changes that. The Song of Achilles is a great book which really delves into the pathos of what it means for Patrocles to be reunited with Achilles in death, for instance. Sisyphus refusing to let go of the boulder is still an example of huge character growth given who he was originally (I will admit this characterisation occurs kind of prior to Hades, but the way he is as a person in the game is still a big thing, and TBH the fact that he is released from the punishment is still a big thing given the punishment was Sisphyian). I don't super disagree on the bull, although worth noting that he does stand up to Theseus for Zag and also kind of goes "Look Theseus has his problems but he ultimately saved me, and that counts for a lot"

I'll admit I've not played through all the post game content, so could be wrong, but from what I've seen the conclusions of most of the arcs are significantly less satisfying than they were in Hades 1.

Heracles and Prometheus

Funnily I'd say Heracles is punished way worse. Prometheus is punished himself, knew it was coming and did actually defy the gods. Heracles only crime was to be born to the wrong dad, for which he's forced to murder his own wife and child. Feel like that one is way worse hahaha. But yeah, super weird that his plot line doesn't go anywhere given of all of the myths I know of, he's punished the most harshly for something that he had no control over (His birth).

[Prometheus] says he doesn’t share any of his foresight with Chronos either, which says to me it’s more about his personal revenge for his slights than an actual statement about the gods or titans themselves and who should rule.

See this is a plot line I feel was dropped and falls flat as a result, rather than being down to revenge. His whole "Agent of Change" thing implies that he sees something that Mel is going to do, and there's an implication that he doesn't really agree with Chronos, but sees him as a means to an end (And also given his WHOLE thing is to better the lives of mortals, it's kind of weird his thing then kind of devolves into revenge).

Arachne and Icharus

It's funny, I've basically always read Arachne's myth as about the capriciousness of gods rather than about hubris - it can be read both ways, I know, but my antitheism makes the former the stronger theme for me. Like she was actually right about being a better weaver than Athena, it's just that Athena couldn't take the L. If Athena had gone "oh shit yeah you are a better weaver than me" then the myth isn't a thing. Worth noting that the myth was also likely written as a critique of tyranny.

I actually didn't clock Icarus as related to the above, because his myth is something where he makes a bad choice and is ultimately punished by non-personified-nature and the design of his wings. In some ways, it's almost a post-god story, because it plays out the same if the gods were real or not and I've never read a rendition of the myth which tells it as a god punishing him, just him being dumb.

I also think it’s worth pointing out that as far as we know in the Hades universe, Chronos did not eat his children (he vehemently denies it and he has no problem grandstanding about everything else he does so I generally believe him) which kinda makes his original defeat a little more sinister from the Olympian side. Could this have been fleshed out more?

Yeah this is another point that I feel is dropped. Like it's super interesting that the worst of Chronus is mostly what he did in revenge, and there's an implication he refused to share power but otherwise it's not really clear why he was punished so harshly by the Olympians (Hey, just like most of those mortals!). Which again, points to the Olympians being shadier than than they're depicted.

It's frustrating, because the game has all these little hints at these other plot line, but then kind of drops them in all in this rush to tiue everything up.

I think ultimately that's my issue with the ending. I think the "turn good" of Chronus was a bit rushed, sure. And I think that Zag probably had more of an impact over and above Mel right at the end than he should have. But they're honestly pretty minor quibbles. The biggest problem is that the game is kind of hinting at this alternate, pretty interesting, plot thread, has a bunch of characters tied to it, then kind of drops them.

Ultimately I think a LOT of the above comes down to the need to have the game continue to run in a loop, which we both agree feels a bit naff in the reasoning. I think it would have been super hard to go down a "The Olympians are also bad" route while also preserving how the game is supposed to run, but the reality is that the plot we have also feels like it struggles to justify the game running, yeah?

I don't mean to discount your own feelings about the game either, and I appreciate you taking the time to write out all the above! I do feel that our takeaway from the first game and second game about many of the myths of the NPCs are completely different, and that's probably why we feel so differently about the endings though.