I really liked the duarte/hivemind plot. It was a logical extension, especially with the revelations about the builders and who they were. To me it seemed like the protomolecule was essentially using Duarte to try to revive the race via humanity, in a sense. I found the ending very satisfying. I also get the impression the sol system was pretty beat down at the end. They clearly still had technology and hadn't fully regressed but it very much gives the impression that things haven't been going well. Amos mentions they're starting to get their shit together so I assume they're on the other side of it now, whatever it was, but clearly the humans in Sol just fell back to their normal infighting.
I don't think anyone really needed an epilogue beyond that. Alex, presumably, rejoined his family and finally (hopefully) got to do what he always wanted to but never could - be a father/grandfather. Naomi went home with Amos and probably tried to help rebuild something, but really didn't have anything else anyway at that point. Holden went out like Holden would - sacrificing himself to save everyone.
Additionally, i thought the science was really cool. The idea that the slow zone was just a bubble of 'reality' inside another universe, essentially stealing energy from it to power all their tech and science-magic. It explains why the goths hate them so much too. The epilogue was pretty cool too - seeing that humanity found another way to go FTL and kept advancing, and presumably we're getting the slightest hint of a humanity ascendant, as FTL travel means they can finally start expanding out in the galaxy without all the baggage and problems of before.