Nasu actually wanted to go the girl main character route because it was different and original. That was until the artist said he preferred to draw Arthur as a girl and Nasu, after seeing the character design of female Saber, agreed so in order for the mana transfor plothax to work they decided to exchange roles and make the main character a guy.
Also, your point of having a female main character becomes void the same moment people began complaining they wanted to control Rin as main character (Rin actually wasn't supposed to be the Tsundere. YOU were supposed to control it. Rin's original design states so, too, saying her and Ayakka's personality ended up "melting" in order to at least have one Tsundere in the game).
You: *starting up the game* Hey great, I wanna fuck girls
Rin: No anon, YOU are the girls
And then anon was a clumsy meganekko tsundere (for King Arthur, non less).