GC555,
Long story short, someone, somewhere, would have heard or felt something. Jason especially. At the risk of another Spoiler Alert, he has eyes and ears in places where The Boss doesn't. The Boss may hold the POWER, but Jason holds something just as important. He holds the INFORMATION.
I'm still trying to find the reference again, but what I read mentioned a compound referred to as "Ramoray's Aphrodisiac". And I think it was created before she joined up.
As for additional storylines, perhaps a mini-quest prequel to LTA concerning the Brown/Church arc? That could also be an entirely new game.
I actually gave up trying to accurately measure game map scale back in the days of Sym Cyti 2@@@. I might dust off My copy of that, and use it to create a map of Lewdville just for fun. The area where the game happens is basically a suburb SE of the city proper. I would be interested in having other areas to explore around the city and it's environs. The trainers have only a finite number of possible recruits within the map area, and sooner or later, that resource will be tapped out. It's like being a pirhana in a guppy tank. Sooner or later, there won't be any guppies left, and the pirhana has a problem...
I'm also honestly surprised that no-one else is joining us in this thread.