From a relatively recent interview with Team ICO's Fumito Ueda:
http://www.1up.com/news/fumito-ueda-last-guardian-trivia-new-projects
Welp, I sure hope he was just joking about his team's "reasoning" for not going with a female protagonist...
Early in development, the main character in The Last Guardian was female, but the team ended up going with a boy. The reason: they thought it would be more realistic that he would have enough grip strength to be able to climb around, and because they wouldn't have to worry about camera angles with a girl who wears a skirt.
http://www.1up.com/news/fumito-ueda-last-guardian-trivia-new-projects
Welp, I sure hope he was just joking about his team's "reasoning" for not going with a female protagonist...