I know there are alot of threads like this and many of them are completely filled with idiocy and people who I think didnt read or skipped many chapters of the manga. >.>
Naruto's parents are Minato NamiKaze (The forth hokage)
And Kushina Uzumaki (A civilian or ninja that originated from the hidden whirlpool from what I understand)
Naruto was born on the day of the kyuubi attack (This might of destroyed the hidden whirlpool and is probably why we havent heard about it in the series or manga) and the kyuubi was sealed inside him by his father, His mother died during childbirth. (At least thats what they say, for all we know some people who had animosity towards the forth or even Kushina herself could've finished her.) Now in more current manga we find out that minato sealed a bit of himself into naruto (A piece of his soul or something?) ONLY to fix the seal if it was to ever break or weaken to the point it did. (The 4th is not sealed into naruto!)
Now Bloodline limits can come in all forms They are not just eye based abilities like sharingan (Copy wheel eye) and byakugan (White/evil Eye). There are others like Haku's Crystal Ice mirrors (A bloodline granting the user the ability to blend two elements, In this case the wind and water elements, And Use special jutsu with this element.) or even kimimaru's (Cant remember how to spell his name.) Dead Bone pulse (I think thats what its called).
Naruto's 'bloodline' I believe could be a mutation of the kyuubi being inside him, His healing ability. Like gaara had the ichibi inside him and could use sand with just chakra and I believe mental command, Even after it was removed from him. (I think he could still use it >.> I need to re-read the manga) It could have been his body adapting to the strain of the kyuubi being inside him, not the kyuubi itself -_- the kyuubi's chakra being of pure youki (Demonic energy/chakra) Is poisonous to humans, that includes naruto, But since naruto has had kyuubi inside him his whole life he could've developed some resistance to it. Like how you can give yourself small doses of a toxin (Non fatal amounts) And develop anti-bodies to that toxin. So he could use it to a degree, his body still breaks down if he uses too much.
Now that I think about it it would also explain his large chakra seeing as his chakra coils had to grow around the kyuubi... Well anyway you guys might say that kyuubi is the ONLY reason he can heal, but you are incorrect as orochimaru had sealed away the kyuubi with a.... 5 point seal? (Cant remember the jutsu name) And he was still able to heal if not a bit slower.
Now I ask you this, does all this not make sense? My theory to these are well thought out and pondered on (Alot of spare time).