Er... I only read AL once, a few years ago. I don't really remember anything much from it, except that I loved Icchan. When I get money, I'll probably buy it and read it again, but it's not at the top of my list. Right now, I'm just trying to round out my Tokyo Babylon and X collection. (Subaru/Seishirou is love. Twisted, creepy, tragic love, but love nonetheless.)
I see your point about how guy-ish Seiya is. If Usagi were to be in a lesbian relationship, it would be with Seiya as opposed to Rei, the other character Usagi is consistently slashed with. I'd also say that Usagi might end up with Haruka since Haruka is also guy-ish, but that would violate Haruka/Michiru. And they are inviolable.
And Seiya, Taiki, and Yaten do have... unique circumstances. It's all Seiya's fault, I'm sure. She's definitely the one who convinced the other two to go trans. Personally, I like Seiya/Kakyuu and Yaten/Taiki; (after all, remember, Seiya pretty much fell in love with Usagi because Usagi reminded her of Kakyuu.) And I do like Usagi/Mamoru. (shrug) They're cute together, and the whole star-crossed lovers in a past life thing appeals to my romantic side. And I've always been a bit of a canonslut; you have to give me a pretty big reason to violate canon for me to support a non-canon coupling.
I also do not see Tomoyo and Sakura actually being together; half because Syaoran and Sakura are very cute together and, after Tsubasa, are as inviolable as Haruka/Michiru, and half probably because Tomoyo rocks my world and I would so date her if she were older... and actually real... (Geez... )