There's actually a really nice article on the making of Clementine in this month's Game Informer that talks about Clementine's character development. They originally planned to have Clementine be the younger sister of the original player character who was a young man who's parents had just been killed and was raising Clem on his own, but this was changed because they didn't want to drop players into a pre-existing relationship, as they didn't think that would work as well in the world of The Walking Dead. When they came up with Lee as the player character, they made Clementine African-American because they wanted it to seem like Clem could be his daughter.
Another interesting thing (although off-topic) in there is that her trademark baseball cap with the letter D on it that was given to her by her father was actually based on a cap that the daughter of the lead artist (Darek Sakai) wears in real life. In fact, Clementine's entire fashion sense (dress with boyish ball cap) is based on Darek Sakai's daughter.