Re: how come naruto has flying thunder god??
A) Naruto has experience with enhancement since he first started using the fox's chakra. Look at any fight where naruto uses the foxes chakra, from haku, to neji, to sasuke, to oro, and so on and so forth. This time it was just much more than he expected. (assuming it was complete speed)
B) is it impossible that the Namikaze line had a bloodline Jutsu? (I know that's not the literal translation, but to me it's the literal meaning so ) his father was highly skilled in body flicker which evolved into FTG. Kushina was highly skilled in sealing techniques. So if we suppose that naruto has had these abilities all along, yet the fox's consciousness was suppressing them... Once he sealed the fox's consciousness bam, his bloodline jutsus kicked in.
The reason the same is not true of KillerBee, is because he tamed his bijuu, he didn't conquer it. where as Naruto conquered the Kyuubi.
Madara/Tobi, for whatever stock you place in what he says, said that the Senju Clan had always lead the village. Hashirama Senju, Tobirama Senju, Hiruzen Sarutobi, Minato Namikaze. I don't remember his reasoning perfectly, and so this may all be tripe (in fact somebody please check that manga chapter for me and let me know if I'm full of it), but, if this is the case and all of the 5 hokages have been senju clan or decendants there of, Then yes Naruto definitely has a relation to the sage of the six paths.
C) Incest vs clans. Many clans marry from within, yet it is not uncommon to bring in fresh blood either. Those who do no inherit the desired traits are ostracized from the clan. Those who do are not. Obito Uchiha was a laughing stock among his clan for being so old and not activating his sharingan. IF only those uchiha were alive today to see Obito's Sharingan able to use MS lol