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Samus Aran said:

Nintendo dresses Link up as a girl and no one cares.

You'd be surprised what you could do with good writers. They could focus on the hardship of coming out of the closet in an intolerant society. You don't even need words or kissing scenes to tell a story like this. You could do it through scan logs of for example space pirates who could mock homosexual people and Samus in particular. They're not the most tolerant society after all. They could also use the American army as an inspiration for how the Galactic Federation views homosexuality (don't ask, don't tell).

We could then get Samus her views on all this through inner monologues during elevator rides à la Metroid: Fusion.

You guys have a way too narrow view on how you can tell a great (back- or side-) story based around someone's sexuality. There's much more you can do then show two girls kissing. You don't even need to introduce a partner for Samus, she could be perfectly single and still be gay.

...two very big problems with that.

One...how would the Pirates even know she's gay? Did Samus have a big coming out of the closet party? Send a postcard to the Federation letting them know she's openly homosexual? The Pirates (and really, everybody else) should be even more in the dark as to her sexuality than we are. 

Two, there's no way to integrate that into the larger story in any meaningful way, mostly because it would be entirely focused on Samus' feelings. The big difference between the interesting dialogue in Fusion and the awful dialogue in Other M is that Fusion's dialogue rarely focuses on her emotions. In fact, the only time she brings her feelings into this is to say that the computer isn't like Adam, and, not-so-coincidentially, that happens to be the worst bit of monologuing in the game. Whenever Samus has attempted to describe her feelings in game, it's come off as very awkward and out of place, and for good reason. It's not solely because Nintendo sucks at writing, it's also largely due to the fact that her character simply isn't one that's built around openly expressing emotion. In fact one could argue that, from what we've seen of her, she consistently makes an effort to keep her emotions close to the vest, so to speak.

Therein lies the problem with building some kind of storyline off of Samus' sexuality. It would need to be based entirely on her feelings, and you simply can't have a story like Metroid where the protagonist's feelings are one of the big selling points. Metroid is based on immersion above all else. You can have a story where Samus discovers information about what's going on, and perhaps even comments on that discovery herself, because the player and Samus are still discovering that information simultaneously. Samus' comments are just an optional tidbit that doesn't really do anything. In a storyline focusing on her sexuality (or on focusing on how she handles the responses to her sexuality), Samus' comments are basically half the story. The way she feels about it is what the story is focusing on. That creates a gap between player and character, a major rift that breaks the sense of immersion.

The idea you've mentioned could be an interesting story if done on its own, but it just doesn't fit into a Metroid game. At all. Metroid stories are focused around being a detective and uncovering what's gone on, not figuring out what some jerk wrote about you on his blog and watching a character react to that.