Disclaimer: I'm in no way authoritative and only speak from my experience.
Sometimes, crossover and unusual pairing are by necessity. My first fandom is Star Trek: the Original series and it pretty have a total of only 2 female characters who're never in the same scene as far as I know. I love Uhura. She's strong, smart and sensible. But I can't find anyone to pair her off. Then I watch Stargate: Atlantis and I fall in love with Teyla. Naturally I pair Teyla and Uhura together. I can easily see them fighting together against the enemy or sit down and talk about culture, language or just turtle soup. It becomes my favourite Uhura pairing.
Sometimes, crossover and unusual pairing are just for fun. Currently I am in Marvel fandom. While I am the last person to suggest that Marvel comics canon is female-friendly (Woman in the fridge, everyone?), its huge cast of characters ensure that there are at least some interesting female characters. There are also chance for two female characters in a title interacting for reasons other than the male characters. Therefore it's easier to pair up female characters. And I have a lot. Colleen Wing/Misty Knight (She 's an ex-New York cop with a cyborg arm. She 's a samurai with a cool katana. Together they fight crime), Carol Danver/Wanda Miximoff (the amazing
garrideb wrote a
ship manifesto about them and pretty said thing better than I would ever do), but I still have quite a crack pairing: Miss America/Golden Girl. They only appear together in an issue but they are comfortable with and clearly like each other. So why not ship them?
Sometimes, crossover and unusual pairing are a protest. Female characters are often underrepresented in the canon. Often we know much about a superhero's father, but never the mother. The only thing we know about the mother is usually her death. For example, Howard Stark play an important role in the Iron Man movie, but we never know about Iron Man's mother. The canon is also bad to the established awesome female characters. Peggy Carter is a spy/reporter in WWII. She's depicted as brave and independent. Then in the recon that we always pretend not to exist the canon has to ruin it. So why not reimagine Maria Stark as a not-so-sociable scientist working alongside super spy Peggy Carter and let them have femslashy spy adventure together? They deserve better treatment than what the canon gives them.
In short, I like crossover and unusual pairing sometimes for necessity, for fun, and protest. I would like to hear your opinions!