Oh Yathzee, you poor misinformed former husk of a human being. Like so many others, you have no idea about what you're talking about because all you did was take a quick look at some Internet pages that thought they "called out" Nintendo being homophobic and let that be it, no deeper look into the case or anything. And thus, you reached a horribly misinformed conclusion.
Here's what actually happened: Tomodachi Life was an installment in a franchise popular in Japan but not released anywhere else. Nintendo thought: "Hey, maybe the kids and some adults will have fun with this too! Let's port it!" and decided to do just that. All was going fine and well, until a certain report popped up that made the "white knights of social justice" mount their horses and cry for Nintendo's head on a stake. The report apparently said that the Japanese version allowed same-sex marriage and that it would be an excluded option for the rest of the world, and that sparked huge controversy and rightfully so. Except the report DIDN'T say that, there was a translation issue. There was A BUG in the Japanese version that made it possible to have people of the same gender marry, but which would also make the game crash, THAT IS WHY THEY CHANGED IT. PEOPLE DON'T LIKE HAVING THEIR GAME CRASH.
But the damage was already done. The Internet cried out in anger, they demanded the includusion of same sex marriage for a game that was already done and was just getting some tweaks so other audiences could play it. It was way too late to make that change, so it wasn't done because it couldn't be done not because Nintendo is homophobic like SOME people like to assume. And before SOME people ask why same sex marriage wasn't included in the series before, and claim not including that makes them homophobic, it's more likely a matter of demand. If the Japenese audiences (those who the games in the series were made for to begin with)had wanted same-sex marriage in the Tomodachi games, it would probably be there already.