1. the idea to spare chronos comes from melinoe. in the normal ending, zagreus spares him and melinoe gets very upset while zagreus tells her to get over it.
2. Melinoe keeps her memories of the alternate universe where she grew up with her family. in the normal ending she was robbed from any sort of happy ending while everyone around her (including chronos) remembers her living happily in the house of hades. we also get a new cutscene showing her grow up with her brother.
3. there’s more dialogue in general to flesh out the ending and her relationship with her family.