Wouldn't it make more sense that X is the female and Y the male? Females have the chromosomes XX and males have the chromosomes XY. Studying names is one of my hobbies and so it wasn't hard for me to come up with possible names for both characters. The first thing I noticed about the female protagonist is her blond hair so I obviously went with that and thought about the names Xana, Xantha and Xanthia that are all Greek names meaning blond. Unfortunately, it wasn't as easy for the male protagonist. The things that stood out the most to me were his cool long hairs and sunglasses but I failed to find anything related to that. I then tried to find two names that fit together like it was the case with most protagonists from previous games.
I went with the themes of sky and forest because of Yveltal and Xerneas who can be seen in the sky and forest respectively. This second tentative proved to be fruitful with the girl because I found many Greek names such as Xyleena, Xylia and Xilyn all meaning from the forest. However, the best thing I could find for the boy was the Native American name Yakecen, which means song from the sky. The problem with that name is that it doesn't quite fit in the English language. Desperate, I decided to reverse engineer my strategy by first focusing on any name I could think of that sounds good. After making a list of names, I tried to find similarities between both genders and I found two. One match was pretty obvious: Xerene and Yen, both meaning calm and serene. The second one is Xela and Yael, meaning from the mountain and mountain goat respectively.
I always used to just pick one or the other based on their looks, but, lately, the games have been going with a "blue is for boys, red is for girls" theme, and color-coding everything from pause menus to Global Link user interfaces. And... I hate the color red.
So, it'll probably be the boy for me. Luckily, he's one of the nicer looking ones. Except for that hat. V_V