Given my predilection for CRPGs set in the D&D/Forgotten Realms ‘verse, probably my favorite “wrong” pairing was a series of fan fictions with Sand x Torio (Neverwinter Nights 2). That was definitely off the normal radar, but honestly, so well written that it worked.
Then there was a mod written for Baldur’s Gate/Shadows of Amn, where the PC gets to romance their nemesis from the original game, their half-brother Sarevok, who spent the entire original game trying to kill the PC so he could absorb the power of their father, the dead god of murder, Bhaal. It was a major enemies to lovers twist, but again, well written enough to work.
I’m not sure I’ve ever managed to write anything so spectacularly wrong and yet as perfect as those two… *sighs*