I don't think Naruto only being half Uzimake, as you put it, has anything to do with it. I am pretty sure that Minato decided that Madara/Tobi was going to be a danger in the future and a possible solution was to give his son the Kyubi's Chakra to help him defeat Tobi.
I don't think Naruto is ready to face Madara right now and we don't even know exactly how powerful Madara is but I wouldn't say that Naruto could never defeat him. I see it as Naruto can get much stronger even than he is now. He has only scratched the surface of his potential. He still hasn't learned any sealing techniques or anything like that and he's only 16.
Minato definitely had some insight about Naruto and the Kyubi. If you notice when Naruto is training with Bee its said that the Minato developed the Resangan just so Naruto could use the power of the Beast Bomb. Minato knew that Naruto would have trouble with the Nine tails and probably wouldn't be able to ever fully merge with it like Bee can merge with the 8 tails. The Kyubi is pure hate and wants to destroy everything so Naruto can't let him have control like the other Jinkuuriki can. Even Bee has trouble controlling the 8tails in full merge form and the 8tails is friendly.
The Kyubi doesn't respect anyone, I don't know why people keep saying that he will only respect a strong person. Minato was strong enough to defeat him and the 9tails still doesn't respect him at all. The 9 tails won't choose Madara over Naruto or choose anyone for that matter he wants to be free to do as he pleases.