I highly doubt it will be remembered that way.
I'm going to put aside the subtle offensiveness of describing people's gender identity in terms of a fashion trend and just say that even if transgender people are edging into the mainstream, we will have to deal with the same problems of stereotypical representations that most other minorities do.
I think pretty much everything the article mentions, aside from maybe the James Franco magazine cover, is just part of a general trend toward androgyny in a lot of fashion, and this is especially true for the urban "hipster" fashion which the NYT seems to idolize. Skinny jeans for skinny guys, baggy sweaters and flannel shirts for even skinnier girls, and American Apparel's insistence on selling "unisex" clothing all kinda contribute to an androgynous aesthetic.
But the year of the transsexual? I don't think so. You could pick out pretty much any year from the past decade and find the "zany" news stories about trans people that this article does, and there doesn't seem to be anything particularly positive happening on any large scale. It seems like the fashion world just kinda sorta loves the outrageousness of Lady Gaga and having a transsexual model, so they talk about it! And that's fine, but to 99% of America and trans people, the change is much more gradual.
As for James Franco, he's just awesomely weird.