I find that Tomodachi Life is a very risque game, and am absolutely amazed that it somehow is getting an E-Rating from the ESRB. And that, my friends, is the exact reason why I suspect Tomodachi Life doesn't have same sex marriage included (that and the whole japan not really being very open to the outside world and not exactly knowing that much about issues outside of itself). I think that given that same sex marriage is considered illegal in quite a few places had it been incorporated it would've easily upped the rating from E to at least E 10+ and probably a T. Which would draw away a lot of potential costumers.
Quite a few people suspected that it may have to do with not wanting to cause a religious riot, but being a Christian myself (and knowing several other Christians that think this next thing I'm about to say I don't think it would've been much of an issue) not a lot of us would really care.
So there we have it. I really think it's just because of the ESRB and not wanting to create a rating that cuts off potential customers for a game that is sort of aimed at a younger audience. Sort of.