Going by the popularity post on the villager trading plaza:
Mott in ?clair and Gayle in Creme, both are bottom of the barrel. I find Gayle extremely cute so I'm surprised she is even considered unpopular! As for Mott... well, he was one of my original five villagers and I disliked him when I first saw him (though not as much as I disliked the other 4) But now I absolutely love him. He is probably my favorite villager in the entire game, probably because I've become such great friends with him <3
In my town it would probably be Rasher and Tabby since they aren't seen as "popular" by others...But I enjoy having them as my permeant ratchet couple and my dreamies