Re: Naruto and "Granny" Tsunade
You have points, but I disagree that all the clans in Konoha are derived from the Senju. While Konoha was founded due to a peace agreement between the Senju and Uchiha, I would tend to believe that the other clans joined up afterwards. The Aburame, Saritobi, Hyuuga, Inuzaka etc all probably found homes under the Senju/Uchiha alliance to gain a stability to thrive. I feel this to be true because Clans usually form from families as a sign of pride - why would someone spurn the utter greatness of Senju to be known as anything else? Also, the byakugan is thought to descend from eye techs similar to the development of the Sharingan. This couldn't have happened in the brief history of the shinobi villages (what - 4-5 generations?).
But I will submit there is little evidence that it is either way - I just am on the side that it is more likely that clans banded together and potentially interbred rather than the Senju clan splitting many times.
As for the passing on of special "genetic" techniques, here's a question: If an Uchiha has a child with a non-Uchiha, will that child develop Sharingan or not? Do all Uchiha develop the Sharingan? It is a fairly unanswerable question until Kishi gives us a situation to this effect, because as much as we'd like to talk genetics of ninja techniques, there's bare evidence to decide how that would work.
New question - has there ever been a picture of a female sharigan user? I can't think of one off the top of my head. Maybe it's Y-chromosome linked... hmmm...