Charlie. There is no dubt. Just watched season 2 and not only does it fit with the timeline. The way she speaks and her mannerisms mimics Miles perfectly. I assume it was a setup for season 3 that didn't happend.
X ~We are the people our parents warned us about
Agree, there are times when she sounds and moves like Miles. Sure you could argue that he was the one who trained her, but still, id say there was a plan for season 3.
--There is no spooon
It was confirmed in the online comic book finale that indeed Miles is Charlie's Father
The Man with the Multitrack Mind-http://www.soundclick.com/bands/default.cfm?bandID=802296