When Naruto and Fukasaku found out something was wrong in Konoha, Naruto was smart to leave kage bunshins in Mount Myobokuzan to collect natural chakra. So he obviously has a great advantage.
BUT! what if Naruto was ambushed? Naruto would not have the same advantage. Naruto could make 100 Kage Bunshins and have them flee and hide somewhere to collect natural chakra, but for some reason I doubt Kishi would have Naruto do this... how do YOU think Kishi would have it?