I don't do the whole shipping thing, just not something that appeals to me. I do have pairs of villagers who I think go well together based on design, but without a relationship aspect.
I've had Ankha and Lucky living in my main, horror-themed New Leaf town because, Lucky being based on a mummy, they both have that ancient Egyptian vibe. Unfortunately, I'm thinking it's about time that I split them up so I can have Ankha in my New Horizons island, which is based on world history.
I also have Octavian and Marina in that same town and like to imagine that they (and I guess Inkwell and Zucker by extension, I just don't care about those two much) are actually aliens from outer space, both because of Octavian's house being based around space and to explain why you can catch octopi from the ocean.
I have Cobb living in that same horror-themed New Leaf town. Due to his green skin, yellow eyes, and the mad scientist-themed interior design of his home, I imagine that he's in fact a mad scientist who made himself undead through some experiment. Tying into Cobb being a mad scientist, I imagine that Stitches was created by Cobb in a Frankenstein's Monster sort of way. Again, another resident of that horror town.
Sterling and Knox are both residents of another of my New Leaf towns, a town that features representatives from across all the different bird species in the series; Bird, Chicken, Duck, Eagle, Ostrich and Penguin. They are the Chicken and Eagle representatives of that town. They're an obvious pair for various reasons, from their names being references to gold and silver, their helmets tying into that and them both being based on knights. I like to imagine that they act as guards for the town in cooperation with Copper.
Another New Leaf town of mine is based around a combination of the circus and a magic show/magic in general. In terms of pairs, I have Elise and Tammi (the Peppy Monkey, not the Sisterly Cub) as residents of this town and they're the circus acrobats.
Other stuff I came up with over the years as "backstory" for certain things:
- Boris, in my mind, is a vampire. Why? His name makes me think of the actor Boris Karloff, who was the man who portrayed Frankenstein's monster in the 1931 Universal Monsters movie and some of the sequels. How does this tie in? Universal was also behind other old monster movies, one of those being Dracula featuring Bela Lugosi. This all ties together (admittedly loosely) because of Boris' tusks making me think of vampire fangs, even if they're on the bottom jaw rather than the top. Maybe convoluted, but I enjoy it. He's in that horror town too.
- Going back to the previously mentioned hybrid circus/magic show-themed town from the Tammi and Elise mention earlier, the mayor of that town is the ringmaster and a stage magician. The idea is that she has a teacher, another player character, who is an actual magician (think of mages from movies and games and the like). I like to imagine that the teacher animated/brought to life a teapot that had the design of an elephant's head, which would explain Tia.
- Pretty simple, I like to imagine that Beardo is a late 1800s detective, like Sherlock Holmes. He had the outfit in New Leaf, and his house in both New Leaf and New Horizons are both pretty professional looking, with the one from New Leaf especially giving me that vibe.
It's fun to come up with these little additions to make the towns feel more full of life.