The source (always remember to check it!) is TheMarySue.com

The whole, original unedited piece is on the source; I've merely quoted some parts of it.

The following piece was written by Brianna Wu. I bolded the interesting parts:

Representation for transgender people is equally tough to find in gaming. Both Dangonronpa and Persona 4 managed to blunder transgender representation. One of the most famous transgender video game characters, Poison from Final Fight, is empowered but blatantly oversexualized. Characters and stories like this reinforce the harmful idea that transgender women only have societal value in their sex appeal.

That’s why I’m thrilled to tell you that one of the most famous women in videogame history happens to also be a transgender woman! It’s none other that Nintendo’s Samus Aran!

It’s true! In 1994, the writers of the official Japanese Super Metroid strategy guide asked Metroid’s developers if they could share any secrets about the intergalactic bounty hunter. Hirofumi Matsuoka, who helped work on the original design for Samus Aran, claimed that she “wasn’t a woman,” but instead, “ニューハーフ,” or “newhalf.” This language has its own issues, but terminology used for gender in the early 90s was as different in Japan as it was in the West.

[...]

However, “newhalf” wasn’t always used in a pornographic or insulting context, especially in 1994 Japan. The term is older, and stems from popular use of the term ハーフ, or “half,” used to refer to Japanese people of mixed-race origin. This form of self-identification became popularized throughout the early 1980s. By 1982 it had been picked up by the press and was used to refer to transgender performers such as actress and singer/songwriter Rumiko Matsubara.

Looking to negate Matsuoka’s remark, some gamers have pointed to a FAQ on the Japanese Zero Mission site by Yoshio Sakamoto, co-director of Metroid. There he says Samus being a newhalf is not impossible, but unlikely. Others have pointed to Samus’s portrayals as a child in Metroid Zero Mission, Metroid Other M, and official manga as proof that she is actually a cisgender woman.

This is where we get into the uglier world of cisnormativity and transgender erasure. Over the years, Nintendo has slowly altered Samus’s design into a petite blond woman with large breasts. Finding her sexually attractive, some gamers are flat-out uncomfortable thinking about her as a transgender woman. As @ThatSabineGirl points out on Twitter, many gamers are incorrectly assuming she is cisgender simply from her gender presentation. The truth is, you can’t know if someone is transgender by simply looking at them. 

Fans asking for ironclad proof of Samus’s apparent transition can suspend their disbelief enough to believe there are bird aliens that develop powersuits, but can’t believe a girl could declare her gender identity at a young age. Besides, this is the same canon that purposefully misgenders the main character in both the Western and Japanese manuals for the original NES release in order to keep her gender a ‘surprise’.

No matter what fans say, the intent of the creator is the only opinion that really matters.

So, what's your opinion on this?