I'm of two minds about this: if we say shipper wars dismiss female characters, are we dismissing fans who identify with the males involved? You're completely right that a lot of shipping comes down to guy A vs. guy B, but there are people out there who identify with the guys more than the female at the center of the triangle (this is the point where I wonder why there can't be more shows like Lost, because they handled the triangle by making it a better square).

I once had the best conversation with a female slash fan, who said she identifies with male characters more because she wants to live the masculine narrative. She doesn't identify with Molly Hooper, she identifies with Sherlock Holmes. She does't ship Molly/Sherlock, she ships Watson/Sherlock. She said it was the same thing with Teen Wolf and Supernatural and all those shows where the slash fans seem to silence the fans of the het relationships. I told her that I'm exactly the opposite. I don't identify with male characters; I identify with female characters, so I either ship slash or femmeslash pairings.

I wasn't thinking in terms of feminist criticism when I wrote this. You're right in saying that female characters often get dismissed in shipping. I think that's because a lot of female fans identify with male characters. I don't know if this is latent misogyny, that they identify with the male characters because society values male characters over female characters, or that there's just something about the male characters that relates to them better than female characters. So while I think you're probably right, I'm also conflicted.