THIS IS JUST WHAT I THINK, IGNORE IT IF YOU WANT TO
Okay, I'm going to look at your icon, and take a wild guess at what character you mean.

I think the most important thing is to keep the feel of the character similar to the way they feel in canon, and work butch/femme back from that. Man!Snake is charismatic and sexy rather than handsome and pretty - he's good looking, but that's second to his sense of presence. His woman self would feel the same way to the other characters. That said, there's nothing androgynous about his canon self (even though he does claim to be a fan of women's figure skating) so making her an ultra-butch woman wouldn't be the answer. Just as Man!Snake's effortless masculinity is alluring to the other characters, Woman!Snake's effortless femininity would be alluring.

Of course, she'd still have to be muscular. Not saying she'd be ridiculously steroidal - even though Man!Snake is big, he's not HUGE because that wouldn't help him sneak around - but I don't think massive tits, while a definite symbol of femininity, is going to be the best way to express it. I'd keep her feminine, but don't be scared to give her masculine physical traits where appropriate, just like Shinkawa wasn't afraid to give Man!Snake long eyelashes, long legs, curvy thighs and an unusually large butt for a man of his body type.

tl;dr LESS EVA, MORE THE BOSS.