While technically madara had more chakra, although naruto has the ability to absorb a tremendous amount of natural energy which neutralizes that advantage, I give it to naruto. The dataflow says naruto'stole senjutsu of the six paths equal or surpasses madara's in certain expects. The manga feats back up this claim. Not to mention he is essentially the Jon of every bijuu, thus giving an advantage to forcefully using the power of the juubi. Naruto has access to the bijuu special abilities. Also being able to add his own techniques on top of the gudou dama as well. Not to mention I just like his design better. His is by far superior. I would say their healing abilities are relatively the same as well. Maybe naruto cant grow back his bottom section if he losses it, but naruto at vote 1 was able to heal instantly from a hand going straight through his chest. That version of naruto cant even be compared to Rsm naruto. So his healing should be on another level as well.