A rare pair even in a megafandom can be pretty tiny! For instance, I ship Scott/Ororo in X-Men Original Movieverse - and I can probably count the number of stories (well, one is a series of short fics, so I count that as one because it tells all one story anyway) I've seen for that pairing on my fingers. (Of course, I haven't been scouring for it lately, but still - Scott/Ororo was rare enough to be eligible for Fandom Growth last year! I know, because I wrote it as my assignment, lol. That means less than 10 fics total for the pairing on AO3.) It's really small. Scott/Rogue is a lot more common, and even that isn't a huge one.
Other rare pairs I ship (from more medium-sized but on the small-size fandoms): Myles/Tara from Sue Thomas F.B.Eye (which isn't a super tiny fandom but it's definitely not big - still Yuletide-eligible since most of the fic for the fandom is hidden away on locked message boards) - and I've seen less than five fics total for it, not counting the YT gift and treat I got (both of which were more friendshippy than romantic) Dov/Gail from Rookie Blue (which isn't so tiny as to be Yuletide-eligible still, but it's nearly dead - except at least one of the tiny handful of authors still posting fics happens to be the one writing the really good Dov/Gail fics, so yay!)
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Other rare pairs I ship (from more medium-sized but on the small-size fandoms):
Myles/Tara from Sue Thomas F.B.Eye (which isn't a super tiny fandom but it's definitely not big - still Yuletide-eligible since most of the fic for the fandom is hidden away on locked message boards) - and I've seen less than five fics total for it, not counting the YT gift and treat I got (both of which were more friendshippy than romantic)
Dov/Gail from Rookie Blue (which isn't so tiny as to be Yuletide-eligible still, but it's nearly dead - except at least one of the tiny handful of authors still posting fics happens to be the one writing the really good Dov/Gail fics, so yay!)