Well if we're sticking to just the FE franchise...
Back when I was a teenager with Blazing Sword, I didn't understand the appeal of Florina as a waifu pretty much because I didn't get the appeal of super shy girls. I'm also not sure what it is about Ninian either, can't say I hate her or anything I just find her to be a less interesting/compelling version of Azura if that makes sense.
I suppose Berkut is technically another one as some people mentioned. After I played Shadows of Valentia I found myself wondering if people really consider him a compelling character they wanted to marry or if it's just because of Ian Sinclair's performance.
For my pick of most surprising, I guess I would have to go with the rhyming Gatekeeper, primary reason for this surprise though is because I actually didn't talk to him when I played Three Houses. I pretty much stuck to everyone who offered a side quest and never even got a chance to talk to him. So by default he definitely makes for a surprise.
Does Kronya really have a fanbase that actually considers her waifu material, or do they just list her jokingly like I tried to start in the Forum Games? 'Cause well... you know...
Going off that one reddit post from earlier, I guess it's kind of surprising to see that Dedue actually has fans as a husbando. He's not really a despicable character in my opinion, but he really comes off as the sort of Dorcas/Bartre character of the game in just being kind of unremarkable in my opinion.
Characters I'm surprised aren't more popular:
I really am disappointed to this day that Tethys isn't a more popular character, let alone waifu. Super strong candidate for being the hottest dancer in the whole series and pretty much everybody overlooks her for some reason. Do people really only know Sacred Stones for its incest?
I wish I could list Manuela in here as well, but after all these years I've come to accept that I'm one among the very few who likes women like her. It helps that she reminds me of Misato Katusragi in a few ways so that sure drew me to her.