I would say my main complaint about the ending of the series is how the interactions with the gods happened. Ferdinand did his plotting, the gods voiced their goals and opinions, while Rozemyne got partially mind wiped and shuffled off into a library and later a white void and had close to zero involvement. Rozemyne, the actual avatar of a goddess, had basically no agency or consent in any of it. Rozemyne may as well have just been a piece of furniture for Mestionora to sit on during all of those discussions and it was extremely frustrating.
Mestionora coming back and communicating with Rozemyne, apologizing for blocking off memories which seemed largely just to spite Ferdinand, and then promising to make Rozemyne a librarian to help with Mestionora's library (unlimited reading time included in base compensation) when Rozemyne eventually ascends the towering staircase would go a long way to improving that relationship.
Ferdinand even thought Mestionora was attempting to hide or obfuscate some other motive she had from him during the negotiations which was kind of a dropped plot hook. If "Save Yurgenschmidt by installing Myne as Zent, and eventually elevate her to the position of minor goddess of librarians." was the ultimate goal it would perhaps make more sense, but I still would have greatly preferred if Rozemyne had been present, conscious, and allowed to express her own will and opinions during the discussions with the gods.