I'm at work and haven't read through the whole discussion, so hopefully I'm not repeating too many points that have been raised already!
Like others have pointed out, though, in fanfic, you're pretty much stuck with the characterization and world that's been given to us. In SGA, I like writing Teyla as a viewpoint character (in fact, I'm pretty sure she's the one I've written the most aside from John and Rodney) but I write next to no Carson or Elizabeth because I'm just not comfortable with their voices. With some fandoms, you're just gonna be stuck with a stable of female characters that don't do a whole lot for you, and from the sound of things, that's the case with you and SGA. And I can't blame you. It's awfully hard to write a character you aren't interested in - you basically have to make them an OC in order to write them, and at that point, they might as well *be* an OC. (That's usually the case with me and Elizabeth, when she's in anything other than a background role. I can write an Elizabeth I really enjoy writing, but she's basically an OC.)
I have certain kinds of characters that I keep coming back to, regardless of fandom. Usually with me, it's smart, sarcastic, funny characters, and emotionally bruised characters, or preferably both at once, and a lot of fandoms just don't offer characters like that among the female cast. Of the fandoms in which I've written actively, there's only one (Dragonball Z I know, shut up) in which my favorite character to write, hands down, was a woman, and - oh wow, I just realized, for the first time ever, that she was a female Rodney! Anyway, she was the *kind* of character that I like to write (funny, brusque, temperamental, blazingly intelligent, always coming up with crazy ideas) and she had a very interesting life to draw upon, even if she was mostly written as a caricature in canon itself.
So it depends on what you have to work with, and it depends on what you find interesting to begin with. There's definitely a different tone to male friendships than female friendships, and speaking just for myself, I find male friendships fascinating in a way that female ones, for the most part, aren't - the lure of the exotic, perhaps? I don't think there's the slightest thing wrong with that.
But I also don't want to be a one-note writer, and I make a real effort in my writing to incorporate little-used characters in addition to the usual suspects (giving Ford a strong role in a lot of my AUs, for example) or to cast my OCs in atypical ways (for example, writing a male nurse, or a female airman, in a bit part) rather than sticking with what's easy - which, let's face it, is putting John and Rodney in a locked room and letting them snark at each other for 20,000 words. *g* In fact, some of my fic, in this and other fandoms, is deliberately aimed at trying to get inside the heads of characters I *do* find difficult to write - that, or filling a gap where fandom doesn't seem to be going. For example, my first long SGA fic ("That Which Is Broken") was written in part because there was a lot of fic that dealt with John and Rodney's rift after "Trinity", but next to nothing that addressed Teyla and Ronon's possibly even MORE severe clash in the same episode, and I wanted to deal with the fallout from that. And I didn't have a very good understanding of either Teyla or Ronon in canon, so I wanted to work with them a little bit and try to get a feel for how they thought.
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Like others have pointed out, though, in fanfic, you're pretty much stuck with the characterization and world that's been given to us. In SGA, I like writing Teyla as a viewpoint character (in fact, I'm pretty sure she's the one I've written the most aside from John and Rodney) but I write next to no Carson or Elizabeth because I'm just not comfortable with their voices. With some fandoms, you're just gonna be stuck with a stable of female characters that don't do a whole lot for you, and from the sound of things, that's the case with you and SGA. And I can't blame you. It's awfully hard to write a character you aren't interested in - you basically have to make them an OC in order to write them, and at that point, they might as well *be* an OC. (That's usually the case with me and Elizabeth, when she's in anything other than a background role. I can write an Elizabeth I really enjoy writing, but she's basically an OC.)
I have certain kinds of characters that I keep coming back to, regardless of fandom. Usually with me, it's smart, sarcastic, funny characters, and emotionally bruised characters, or preferably both at once, and a lot of fandoms just don't offer characters like that among the female cast. Of the fandoms in which I've written actively, there's only one (Dragonball Z I know, shut up) in which my favorite character to write, hands down, was a woman, and - oh wow, I just realized, for the first time ever, that she was a female Rodney! Anyway, she was the *kind* of character that I like to write (funny, brusque, temperamental, blazingly intelligent, always coming up with crazy ideas) and she had a very interesting life to draw upon, even if she was mostly written as a caricature in canon itself.
So it depends on what you have to work with, and it depends on what you find interesting to begin with. There's definitely a different tone to male friendships than female friendships, and speaking just for myself, I find male friendships fascinating in a way that female ones, for the most part, aren't - the lure of the exotic, perhaps? I don't think there's the slightest thing wrong with that.
But I also don't want to be a one-note writer, and I make a real effort in my writing to incorporate little-used characters in addition to the usual suspects (giving Ford a strong role in a lot of my AUs, for example) or to cast my OCs in atypical ways (for example, writing a male nurse, or a female airman, in a bit part) rather than sticking with what's easy - which, let's face it, is putting John and Rodney in a locked room and letting them snark at each other for 20,000 words. *g* In fact, some of my fic, in this and other fandoms, is deliberately aimed at trying to get inside the heads of characters I *do* find difficult to write - that, or filling a gap where fandom doesn't seem to be going. For example, my first long SGA fic ("That Which Is Broken") was written in part because there was a lot of fic that dealt with John and Rodney's rift after "Trinity", but next to nothing that addressed Teyla and Ronon's possibly even MORE severe clash in the same episode, and I wanted to deal with the fallout from that. And I didn't have a very good understanding of either Teyla or Ronon in canon, so I wanted to work with them a little bit and try to get a feel for how they thought.