It's not as though
that's the only problem with it. It just seems like bad fan fiction, where one joke that was funny because it was so brief and so unexpected gets expanded into an entire episode, and a character's idiosyncrasies get a baroque explanation that forever changes and subverts the character. To me that's exactly the kind of episode that makes a show feel like it's ready for cancellation.
I like the beginning, but at the scene where Homer is walking Flanders through the house they built for him the show goes off the rails, which is a pattern that many later episodes would follow.