1st Statement
"Nintendo never intended to make any form of social commentary with the launch of 'Tomodachi Life.' The relationship options in the game represent a playful alternate world rather than a real-life simulation. We hope that all of our fans will see that 'Tomodachi Life' was intended to be a whimsical and quirky game, and that we were absolutely not trying to provide social commentary. The ability for same-sex relationships to occur in the game was not part of the original game that launched in Japan, and that game is made up of the same code that was used to localize it for other regions outside of Japan."

1st statement summary: We weren't trying to offend you so don't be offended. That's how the game was in Japan and we don't care enough to fix it for you.

2nd Statement 
We apologize for disappointing many people by failing to include same-sex relationships in Tomodachi Life. Unfortunately, it is not possible for us to change this game’s design, and such a significant development change can’t be accomplished with a post-ship patch. At Nintendo, dedication has always meant going beyond the games to promote a sense of community, and to share a spirit of fun and joy. We are committed to advancing our longtime company values of fun and entertainment for everyone. We pledge that if we create a next installment in the Tomodachi series, we will strive to design a game-play experience from the ground up that is more inclusive, and better represents all players.

2nd Statement Summary: were sorry.  We can't change this version but we do want you to be a part of our fun community so the next will be made from the ground up to better please those we have left out.  

It's like Night and Day. 

I don't have a problem with people asking Nintendo to be more inclusive in regards to sexuality, as long as they don't demand, force, or try to litigate it. I personally praise the developers who aim to be more inclusive, rather than scorn the ones that don't.

You can't have same sex marriages in any game that I am aware of. At least without a hack. I am sure it will happen at some point, but do you really expect some obscure Nintendo Animal Crossing type game to be the first game about gay marriage? Why are the expectations so high for this game but not any others?

In this age of "acceptance" why can't we just accept the fact that it's not a feature of the game? I have no problem with same sex relationships, but I'm also ok with games not touching this subject. It's a kids game, so it doesn't really need to be there. I don't need to explain to my little ones why there are two guys or girls in a relationship in any game. A man and a woman, or a boy and a girl is something that doesn't need to be explained, as their parents are just that: a boy and a girl. Again, I have no issue with homosexuality, but I personally don't see a need for it in this game. It's nintendos game, they can do what they want.

Skyrim!

The "it's only" thing is so sad.

Fable.

The main issue however is the discrimination and hate towards that minority group in the worlds society, there is going to be allot of pushing and shoving for that subset of users to get attention and acceptance, we saw it with Women, we saw it with those who didn't have white skin colour. (Although, discrimination of both still occurs today, just on a far far smaller scale.)
You can bet they were vocal when they didn't have equal rights.

However, I do agree, it should be up to the developer/publisher whether such things should be included.

Rubbish.
In general Homosexual men generally have unprotected sex due to the lack of fear of getting anyone pregnant, converesly they also have more partners.

The amount of diseases that affects those who are homosexual or heterosexual is the same, the chance however is higher, due to the aforementioned issues, but don't blame that on gay men, blame that on society.
Afterall, it's straight people who keep having gay babies then discriminating against them.

Sexually transmitted infections are a reality for everyone...
Condom use is as inconsistent among heterosexual populations as among gay populations and education on condoms is inadequate in large parts of the world (even the developed world)...
But how is this even relevant to a discussion of diversity representation in video games???
It's as irrelevant as a discussion of Tomodachi's genre...

Though I do mostly agree with you and have noticed gay activists being over-sensitive sometimes and pickinng fights with anyone and everyone lately, I don't agree with this last point of yours. Sure, there are alwats more important matters that deserve our attention. Most of us here have huge backlogs and complain about not being able to buy the 4th game we want for the month. Shouldn't we be donating some of that money to charity/Red Cross,etc? There are always more important causes, but that doesn't mean that the we should leave everything else for later. 

The way I see it, this is not so much about Tomadatchi alone, but by making a bid deal about it, Ninty might improve the sequel by offering more options to the players or other companies can hear about it and consider incorporating some gay elements in their next game. For all we know, a developer might make a game with a gay protagonist, which to my knowledge hasn't happened to this day. Why is this important? Well, it's not the end of the world, but it can mean a lot to the LGBT community. Imagine playing your entire life video games where the male protagonist always tries to save the prince or has a male love interest. At some point you'd find a change (i.e. a female love interest) refreshing. And for teenagers who struggle with their sexuality the fact that they can see gay characters in a video game, can help them come to terms with their own sexuality. 

I haven't followed this carefully, but it seems to me that the people who complained to Ninty were doing it as a form of request rather than picking a fight with them.

So, how would you guys implement homosexuality into a game like Tomodachi Life? Would you ask the player about each Mii's sexual preference in the creator? Or would each Mii generated have some chance (50%? 10%? 2%?) of being homosexual? Or would all Miis simply be bisexual and have an equal chance of forming relationships with either gender?

I think I've come up with a solution: Miis should not have genders. As it is, choosing male or female does not affect the assets available for customization. Players could simply create a Mii that looks and acts however they want, and it wouldn't need a defined gender.