Sometimes I wish the "hair-fashion" for young males of Leonardo's time would have looked like the one from the 50s, so these confusions (male or female) wouldn't get so much attention and we could talk about other aspects
(btw, since I've mentioned the 50s there's an old American TV film where the young James Dean played John: http://de.youtube.com/watch?v=21bqgY5HLPw
- after 3:33 min
I think the popularity of the "Brown-interpretation" is partly based on a rather modern idea that every disciple of Jesus was guy with a beard and clothes that look somehow "Middle Eastern". I mean, if you compare the traditional depictions of the disciple John with the way we remember him from several Jesus-movies then you understand what I mean. Though it was not alway like this, the John from an older Jesus-film by Nicholas Ray ("King Of Kings") was still representing that youthful image of him:
On the other hand a rather recent movie that is even filmed from his perspective ("Gospel of John") makes him look like that:
So people that are getting used by this interpretation and not knowing or forgetting the traditional way and therefore not expecting someone looking so young. One could even speculate, whether a young John that is very close to Jesus makes those many Christians, who are scared of anything that goes into a certain direction
, feel uncomfortable, and that they maybe even prefer to see Mary Magdalene next to him.
And of course the old question 'what is actually feminine' rises again. That cuteness is seen primarily as something "feminine" has a lot to do with the fact that youthful looks just stay a lot longer with females, which makes people believe it would therefore a real female trait, while it is actually more a question of age and development.
Just like faces of very old women (or extreme body buidling ones) can look quite coarse (including some growth of beard and often lowered voices) on the one hand, boys would be still on their way to develop all these physical chracteristics that one expects from males on the other. One should mention that this kind of "über-youthfulness" were also attributes of other saints and of course of angels (they idea that the latter look like young males isn't just connected to some art schools of the Renaissance but also based on the bible and a comment of the Jewish-Roman historian Flavius Josephus about the destruction of Sodom).
Here are two examples:
St Sebastian by Raffaello:
St George by Mantegna:
The legends say they were both soldiers of the Roman army so ones would expect them to look more adult, but artists (both older and younger than Leonardo) prefered it to paint them in a way that looks "feminine" to modern viewers. Well, it's not just John, but also other males that got this physical chracteristics. Another strong indication that there was never an intention on Leonardo's side to put Mary Magdalene into this picture.