Naruto rather handily. I can't believe I'm saying this about Naruto vs a Juubi Jin...
Anyways:
1. He has his own Gudou Dama, and actually has more to "play with" giving him a more absolute defense, but Obito doesn't have any pure Senjutsu to damage Naruto, so Bijuudama's from Obito won't harm Naruto at all whereas Naruto is essentially the peak of Senjutsu in the Narutoverse and all his attacks will be threatening to Obito.
2. Naruto is most likely faster as he reacted to an even faster character than Obito, in Madara.
3. All of Obito's Gudou dama are effortlessly smacked back to himself by Obito as in canon, Naruto did it to Madara, a superior form of Juubi Jin Obito.
4. The full power and variability of the Bijuu's powers usurp anything a Juubi Jin, even someone like Madara, could handle. Not only does Naruto have the benefits of a Juubi Jin, but he also has the Bijuu's variety in power, leading to far more powerful combo's against Obito laced with the strongest Senjutsu in the series.