Have you checked the examples I provided?
I would really like to know which are these games you talk about, because in my years of gaming all JRPGs had the same structure of the PC being "special" or as we say on the West: The Chosen One.
FF breakdown of the effeminate villain:
FFVI- The first years after playing it I though Kefka was a woman he's a man
FFVII- Sepiroth with his long flowing hair and bishounen features doesn't look the least effeminate to you?
FFVIII- Seifer Almasy, who looks like David Bowie.
FFX- Seymour Guado
Seifer is as brawny and manly a specimen as you'll come across in FF8. FF9s Kuja is a better example, I think. I mean, the dude wears hotpants!
Androgyny is pretty commonplace in most JRPGs. I'd prefer a happy compromise between femininity and rugged beefiness but hey, that's just me.
Incidentally, HCBailly just began his FF8 Let's Play. Promises to be good fun.