I should clarify that I don't think it's because it's because Japan is amazingly progressive about gender. (After all, this is the game where he gets groped by :biden-troll: who exclaims "You're... a man?!)
It's just that Japanese character designers can go "I think the dudes can and should be pretty too"
As much as I don't like MGS4, I did like that it's one of the only instances where they try to make an aged character feel old and decrepit. Usually they just slap a BADASS BEARD and gray hair on a guy and have like a few token jokes about them getting too old for this or that shit but otherwise they play exactly the same.
Instead of the BADASS BEARD, Snake has a positively hideous old man stache in MGS4. That took balls