So we all know that the Tenth Doctor's daughter looks a lot like the Fifth Doctor, for some strange reason. But have you ever noticed how much the First Doctor's granddaughter resembles the Ninth Doctor? What's up with that?
My personal theory: The Doctor's Gallifreyan DNA contains the code for not just what he looks like at the moment, but any potential appearance he might have at any time in the future or the past. So his offspring may not look like he looks now- they might look like he used to look, or like he may look one day in the future.
Either that, or it's just one of those things.