Given the two ships you've mentioned, I've noticed that you're shipping the main male character with the what can be considered the most featured female character.

Perhaps it's carrying over from the days of fairy tales/popular stories from youth where that's usually the formula--and you're mind has just become geared on pairing them because it was always right in the days where you were getting your feet wet with shipping. I feel like a few shippers I've talked to who ship similar unpopular pairings where this formula (and its opposite: main female with most featured male) get it from because in the majority of their favoite ships, it's almost always the exact same pattern.

I mean, at least with House and Cuddy (as much as they churn my stomach, no offense) the writers are playing with it. They tease you with it and have them toy with the idea. Harry and Hermione...well, I got nothing for you there because I've never seen any sort of spark there and Rowling at best threw you an evil!vision kiss as if she was making sure you knew it wasn't her cup of tea.

idk, just a theory to go along with your "why?"