- SPOILER - Show Spoiler
- It is generational, every few generations they would reapear, the last time was Madara and Hashirama. However Madara tried to cheat by obsorbing some of Hashirama's cells he tried to become both. This WOULD have made him be as powerful as the sage of Six Paths as he would have the powers that were divided. It was less then completely sucessful, and he still died. This is why he had the Rinnigan. He made the mistaken assumption it required Uchiha and Senju blood. Uchihia are direct decendents as the elder son of the sage had the Sharringan, And the younger had spirit... (nothing inate, but the silly power of friendship). However it is touched upon a few times that the Uzumaki clan is a splinter clan from the Senju clan. They still intermarried a fair amount and held 'Strong ties.'
Since the Senju are likely the line from the younger son, and the Uzumaki are connected to the Senju it stands to reason that Naruto would have this potential as well. As a result Naruto and Sasuke still show up, but the potential was hampered significantly. This is why it took so long for both to reach full potential. We do get Massive hints early on when he is taming the Kyubi and later in the war that he has power over trees, the same power that Hashirama held. This could be a spill over from the reincarnation of spirit thing.
As more backup in regard to the Uzumaki thing remember that even the design of the leaf symbol down to the chunin flakjackets caried homages to the Uzumaki clan and Uzugaikure. There was also a Shrine that belonged to the Uzumaki clan in Konoha which shows that there were likely far more Uzumaki in Konoha then just Kushina or Mito.
Thus is another circle in the chain. Just like Madara and Hashirama before them Sasuke and Naruto carry this spirit.