Why aren't Kyuubi and Naruto real allies?
If by "Naruto Vanilla" you mean the manga, then


   Naruto and the Kyuubi actually did become allies in the later parts of the manga. As it turned out, just about all the Tailed Beasts, including Kyuubi, were mistreated and abused by humans, so they distrusted and disliked humans. That's why Kyuubi wasn't that friendly to Naruto, or at least at first.