I've started up a new story because this one has been bugging me for a while. Here's the prologue. And before I start Disclaimer: if I owned Naruto he would have a harem of EVERY girl from the manga except Sakura they are more like brother and sister now.
There are many bloodlines that are well known. Such as the sharringan, that is able to copy your enemy's movements and any jutsu you may know, it's able to detect and dispel genjutsu. It has three levels. The first slows down movement. The second lets you copy your enemies movement and slows stuff down even more. The third allows you to see through genjutsu. There in lies a fourth though. If you kill your best friend then you get the power over the darkest flames of hell named after the goddess ameterasu (spelling?) The second attack is tsukyomi the strongest genjutsu. Where you take somebody into your mind and torture them. There is also Susanoo, the ultimate defense jutsu. But with every gift the mangakyo sharringan gives it requires the sacrifice to use. It causes blindness to its user. Only by ripping out the eyes of your brother are you able to bypass this weakness. Yes the uchiha is brutal.
The Byakugan is another dojutsu that allows the ability to see almost three hundred and sixty degrees of vision. It also allows the user to see through solid objects. They are able to see the chakra network. The dark secret of the hyuuga clan is that they are unable to release much chakra at a time limiting them to taijutsu for the most part.
The kaguya clan carries the bone pulse. The ability to use their bones as weapons. This often causes tuberculosis. The clan itself is brutal in its training. Children are locked in cages for years on end to break them of their emotions. The kaguya are battle happy.
Of all the bloodlines there is one that is darker than all the others, the blood pulse. The blood pulse allows one to control their blood. You can't kill them by any means except decapitation. Their blood comes with a family curse. If a set of twins are born then they have a bond but if it's a boy and a girl the boy develops the strongest sister complex imaginable. He will do anything to protect her, and if he fails then he slowly caves into madness. He will grow cold and often uncaring and ruthless to anyone a threat to his sister or him finding her. They are naturally psychotic to an extent. They are without fear; they are merciless on the battlefield. They are the perfect soldiers of whirlpool, the Uzumaki. There was one deserter before they got killed off. Kushina was the most loving of the Uzumaki. Unfortunately this was seen as week in the Uzumaki clan so she defected to konoha. After she ran to konoha she suffered many horrible forms of interrogation. She nearly broke. Until a man by the name of Namikaze Minato rescued her. They eventually fell in love.
These clan's all are cursed. The uchiha requires life sacrifices for the advanced sharringan. The hyuuga requires the sacrifice of most jutsu. The kaguya requires the sacrifice of one's health for the most part and the Uzumaki requires the sacrifice of being completely sane, especially for twins.