I'd love if we get something like that 2nd ending you are proposing/hoping for
I just would hate to see a show that has depicted mental health and suicide in such a careful and thoughtful way to switch gears towards "the reason shyt is worse than before is because of an evil AI gone rogue". I'd be less worried about things going south if Acca's daughter wouldn't have made Frill's mouth thingy before confessing her love to Ur Acca and killing herself that same night. Now, that can still be explained in a responsible way that makes sense within the show's own logic but it also leaves the door open for thing going in a bad direction. After watching enough anime, I've seen good series crashing down in the last episode(s) for different reason. I really don't want this to happen with WEP.
The fantasy elements aren't the core of the show and I'm fine if some questions are left unanswered considering there's so little time left. And to be honest I'm content with them explaining that the Egg World started because two scientific geniuses became obsessed with teenage girls suicides after the daughter of one of them killed herself without her family having any clue why it happened. So they turn their work into trying to find out "how" the fear of death works and what role their rogue AI plays in that.
The Thanatos and Eros stuff is also something that could be used in a very interesting manner OR as a cheap way out to end the show.