Villian of the season is stretching the premise a bit too thin for me. But it's the same way in the books.
It's still not bad, just starting to fray.
I'm not sure how to fix it realistically. Bookwise it would be a change of pov, but that comes with its own trouble. You can't delve into the protomolocule too deeply, or the precursor civs. That negates the central mystery and threat.
All you can really do is get into the grit of political structures. Which they're trying to do and have an adventure story along the way.
It's not bad, it's just a tough spot in the story. They can extend it forever. But how to keep it interesting.