You have to remember that the Rikudou Sage split his powers within both of the sons. Maybe along the lines they got together mated.. But ancestry is a mixed thing. Neji Hyuuga could probably find some small Uchiha blood along his ancestry. Also, it seems that the Uchiha clan were very limited. They were a tight based clan. Meaning only Uchihas could marry Uchihas, it was incest basically. So Uchiha blood was limited, while the Senju were probably more carefree.