Here at a Q&A session with Team Ico’s Fumito Ueda, he revealed that the non-animal character in The Last Guardian was originally supposed to be a little girl. He said that changed his mind for a couple of reasons.
The first was an issue of believability. With the character having to do a lot of climbing onto the Trico animal and other in-level surfaces, a young boy would have slightly better grip power than a little girl. You wouldn’t be feeling like you were putting a little boy out as much as you would a little girl.
The other reason has to do with….well, a little girl would be wearing a skirt, which you could probably see up with some camera situations. Pervert.