'Making changes is not unusual'
With all the controversy surrounding Fire Emblem Fates (what arena of gaming doesn't have controversy surrounding it these days?), Nintendo has finally spoken up on the matter of same-sex relationships and the dreaded drugging issue. In short, they've confirmed that the game will have the former, sans the latter (which wasn't really the case to begin with).
Speaking to Siliconera, a representative for Nintendo stated:
Making changes is not unusual when we localize games, and we have indeed made changes in these games. When we localize a game we do so in order to make it appropriate for that particular territory. All our choices were made from that point of view. In the Conquest edition a male main character created by the gamer can pair up with another male character (Niles) which ultimately leads to marriage. Similarly, in the Birthright edition, a female main character created by the gamer can pair up with and eventually marry another female character (Rhajat). Like married couples of the opposite gender, these same-sex couples enjoy the stat boosts that come with marriage, which means when they are paired up in battle they are stronger than when they are apart or paired up with another character. In the third edition, Revelation, that will be released as DLC in the eShop on March 10, a same-sex marriage is possible regardless of the sex of your main character, as both Niles and Rhajat can be encountered in this edition.
In other words, like many games that are localized for the west, content might be altered for a different audience. It's a definite shift from their stance on Tomodachi Life, where same-sex relationships were not included by default -- and a glitch was removed that technically made them possible (among other bugs that were mixed in).