Which is an old game!
Fire Emblem: Seisen no Keifu, from the Virtual Console ONLY for the New 3DS. I've always wanted to play it, so it was a great coincidence that I happened to have a New 3DS to play it on.
And yeah, the 3DS Fire Emblem games are not the only ones where character romances ended with child units. Except unlike If/Fates, the characters don't just mate with anyone of the opposite sex and don't abandon and abuse the kids by throwing them into convenient magical dimensions after having sex without any decent plan of what to do if they got pregnant.