If Naruto wasn't the Kurama Jinchuriki, his chakra levels probably could've been lower, but they wouldn't have been much lower - as the Uzumaki Clan are already renowned for having high vitality and powerful bodies in their own right, similar to those of the Senju, and Naruto is still one of the Uzumaki. On the flip side, though, his chakra control would've been a lot better, as the Kyuubi wouldn't be disturbing it or anything. As a result, he could've done a lot better at actually learning techniques, and passed earlier in the Ninja Academy too.
I'm pretty sure that Naruto could've still mastered Sennin Modo. If anything, his Sennin Modo would be even better than in the actual manga, as the Kyuubi wouldn't be there to prevent him from fusing with Fukasaku and Shima, and thus Naruto would be able to attain a permanent SM. Outside of KCM and BM, he'd arguably be even stronger than he is in the manga, at present. Things would be quite different for Sasuke, though, and I'm going to explain why. First of all, one must remember the nature of their different powers and bloodlines.
It has already been confirmed in the manga that Temporary SM Naruto = MS Sasuke. If Naruto wasn't the Kurama Jinchuriki, he'd have a permanent, long-lasting Sennin Modo. Sure, Naruto might need more time to master Sennin Modo (in the absence of Kurama), but in the end, he'd still be on top of Sasuke. If Sasuke hadn't taken Itachi's eyes, on the other hand, he'd have a regular Mangekyo Sharingan that would eventually lose its light and go blind. I guess you all know what that means for the legendary rivals in the end, don't you?
So, in the end, it would chalk down to Naruto still going strong and having access to a permanent SM, while his rival Sasuke is stuck with a regular MS that eventually loses its light and goes blind, effectively preventing Sasuke from being a shinobi any more - that is, until or unless he learns to fight blind or something, and I'm not sure if that's even possible for a Dojutsu user. At any rate, he would never be able to fight as well as he could when he still had his eyesight, and he'd still be inferior to Naruto in the end, just like he is now.
So I'd say Sasuke would be the faster learner of the two, and for that reason, would succeed in the short run. However, Sasuke would end up going blind in the long run due to over-use of his powers, so he'd still lose in the long run, while Naruto is still going strong and ultimately ends up with an even stronger SM than the one he's currently using in the manga. So, in the end, I'd say Naruto was probably the one born with more potential. Being the son of a Kyuubi Jinchuriki and Uzumaki on one hand, and the legendary genius Minato on the other > being the son of some random Uchiha dude and dame. Even if you take away the Kyuubi from him, you can't take away Kurama's influence on him through his mother.
Also, one can't forget the fact that part of the reason that Sasuke has grown 'so powerful', is apparently because he was given performance-enhancing drugs by Orochimaru during his training in Part II, which enabled him to train and become stronger in a shorter period of time than normal. Naruto, on the other hand, has never taken any drugs or anything. If this is all true, then it makes Sasuke look even worse in comparison to Naruto, both in the real manga and also in a scenario where neither would have access to their ultimate power-ups.
If you include EMS as a part of Sasuke's potential, then you'll have to include being the Kyuubi Jinchuriki as a part of Naruto's potential, too. If you include Rinnegan as a part of Sasuke's potential, you must include having the rest of the tailed beasts as a part of Naruto's potential, too. That is the nature of their power-ups in comparison to each other.
