Advice and Trust has a large and vocal fan contingent that actually quite likes the idea of Asuka and Shinji giving Rei the "Israfel Special". Doing It Right This Time and Neon Metathesis Evangelion were both written as a result of wanting to see said pairing come to fruition. (The author of Advice & Trust took this really rather well, by the way, and has in fact commented favourably on both.)
A Panty & Stocking with Garterbelt and Narutocrossover called Angels and Ninjas has many reviewers wanting a Naruto×Stocking pairing rather than Naruto×Panty and Sasuke×Stocking note the premade pairings due to the fact that Naruto and Stocking obviously have better chemistry, spend a considerable amount of time together, get along better than Naruto does with Panty and Stocking does with Sasuke and that's not even mentioning the fact they share a bed.
The story manifests an example of this trope, with a strong Bucky×Natasha dynamic woven in, despite the fact that the fic as a whole is heavily based on the Marvel Cinematic Universe, with not even a tiny bit of Bruce×Natasha chemistry (despite it being MCU canon).
Relatively early on, the author created a poll out of curiosity to see who fans would prefer Harry to be with. Jean Grey won by a clear margin, with Emma Frost and Hermione Granger not far behind, tied in second place. Based on Word of God, Harry's not going to be paired with any of them — Jean Grey is his cousin and Cool Big Sis, though a letter written by a version of Harry from the future notes that she's 'disconcertingly attractive' and pretty definitely shipped with Scott Summers, Emma Frost and Harry are stated not to get on at all and the narration has on more than one occasion noted that Harry very rarely notices that Hermione is female and is 'about as attracted to her as he is to mould'.
Later, he did another poll. This time, Carol Danvers got nearly half the vote, with Diana getting just under a third, thanks to Carol and Harry's vast UST. So followed a lot of cryptic remarks, an insistence that they would be Just Friends, and a grudging acknowledgment that the Portmanteau Ship Name, 'Carry' was cute. If it wasn't clear enough where reader enthusiasm lay, this ship's name was one of three, for a couple that hadn't even had an Almost Kiss at the time (the other two were 'Harol' and 'Magic Lantern'). Eventually, despite his original plan of Harry/Ginny being canon, then something else vague that he hasn't really elaborated upon, he threw up his hands and gave in to the inevitable, And There Was Much Rejoicing among the fanbase.
The Draco Trilogy's main pairings on paper are Harry/Hermione and Draco/Ginny, but readers quickly latched onto the idea of Harry/Draco instead (due to them developing into something resembling Heterosexual Life-Partners), to the point of getting some Ship Tease in the story itself. Considering just how significant the story was in forming common Fanon, it ended up being a major cause for Harry/Draco becoming a Fan-Preferred Couple in the overall fanbase as well.
Ethos/Mukuro is popular, despite the fact that Ethos is already in a relationship.
Quite a few anons like the idea of "Biotherapy" (Kyoji/Miaya) more than the teased Kyoji/Mikan. The two were the closest to each other out of everyone in Class 75, often cleaning up the messes left behind by Maverick, and Kyoji does consider her one of the most important girls in his life alongside Mikan.
Happens In-Universe in the South of Nowhere story Romance on the Set. Spencer was originally cast as the main character Mandy's love interest, but fans of the show preferred Mandy with the Perky Goth Rachel instead.
Despite being a killer, burned dream-demon, many readers of Tainted Dreams would rather see Helyse being with Freddy Krueger than with Jonathan. AnaShadowWolf (the author) went so far as make a poll during the fic to know with whom the readers wanted to see Helyse with. Freddy won. By a large margin.
To Hell and Back (Arrowverse): In the earlier chapters, a number of readers suggested the possibility of Oliver/Kara or Tommy/Kara, despite Oliver already being slated to be either with Laurel or Nyssa, while Kara remained single. The author permanently sunk former by reiterating that none of the three leads (Oliver, Barry, and Kara) would be paired with each other, and sunk the latter by informing readers that, like Kara, Tommy wasn't getting paired with anyone for plot reasons. They later went back on their word by pairing Tommy with Isabel, though they did clarify it was for the sake of the plot than any genuine pleasure in the pairing itself.
In The Vampire Diaries story "To Build A Home", reviewers preferred Stephanie with Klaus rather than her canon love interest Jeremy. The fact that they dated in the past (despite her not remembering it) factors in.
A Very Potter Musical: An invoked case as the show still uses the Official Couple from Harry Potter of Ron/Hermione, yet plays out with the creators' own preferred couple of Draco/Hermione, which as a result has expanded even more.
prefer Itapan over Gerita. There are plenty who also like Geritapan.