If I remember all of this correctly; Back then there was this movement within the backer community that wanted Call D to be used as a villain in the game due to the fact that she resembles a little girl version of Dr. Wily. They even created an entire blog dedicated to it as well.

Eventually Inafune saw this and practically went "Sure! Why not?" on it. Partly because he saw that there was actually a fan following forming around her and the fact that he was the one who designed it. Eventually she started popping up on their update posts starting with this Dev video.