No longer on mobile, so easy typing (and bold/italicized text) all the way:
Niles/Leo
What I like: Could be extremely kinky between the master/servant dynamic and Niles being Niles, also makes for a nice OT3 if Odin joins in.
What I don’t like: The aforementioned dynamic has a disturbing side to it as well, even more so than Sephiran/Zelgius.
How I ship it: Probably more as an OT3 because they could really use Odin to lighten the mood, but it could theoretically work on its own. The circumstances of their meeting could be vastly better, of course, and it’s probably doomed in Birthright where Leo has to be king and so have even more authority over his subjects.
Sothe/Micaiah
What I like: The parallel with Ike/Soren (yes, again) that shockingly even gets mentioned in text, plus the fact that for a cover art het ship it’s surprisingly disturbing if you think about it for more than five minutes.
What I don’t like: The player can opt out of the pairing so as not to impede the free-for-all support style of FE10, which is just weird considering how many moments they get in the main story.
How I ship it: As a marriage that’s probably more than a little uncomfortable for Sothe, both in his suddenly becoming the consort to a queen and that his new wife is the woman who raised him from early childhood. Their later years will be even worse, with an elderly Sothe being supported in his dotage by someone who still looks like jailbait. Eesh.
Heather/Nephenee
What I like: Hey, Heather’s not as much of a predator as a casual read of her character makes her out to be. And for all that some fanboys love her Nephenee is quite available as a romantic partner.
What I don’t like: Thanks to Heather not existing in Path of Radiance they have like two short scenes worth of dialogue.
How I ship it: Easy, they go back home to their village after the war, stuff happens, and Nephenee now has much more pleasurable things to blush over.
And now for an extra FE one of my own, chosen more or less at random:
Eliwood/Hector
What I like: This may have been the first FE pairing I was aware of liking, even before more obvious FE7 picks like Raven/Lucius. They have a warm and touching friendship that’s essentially the emotionally core of their game.
What I don’t like: FE6 dooms this pairing in multiple ways, at least in the sense of them growing old together as a couple. Not that doing so would have been realistic given their positions, anyway….
How I ship it: Mostly as a romantic friendship in the traditional sense, though I could them coming to an arrangement where they meet every so often and their wives understand (their wives can potentially be sisters after all, or Lyn who knows them both very well). They still won’t last because Durban said so, but they’d have a few more years together watching their kids grow up together and develop a quasi-incestuous romantic bond like Naga (St. Elimine?) intended.