Naruto Vs. Pain.
First off, I'd like to say that even though Pain used up chakra, we never heard about him being low on chakra until AFTER he was fighting with Naruto. Not only that but Pain stated himself that nobody ever gave him such trouble.
Naruto got info on Pain? Akatsuki has had about 3 YEARS of time to observe Naruto. Zetsu has been creepin on every fight since Sasuke as far as we know. Otherwise, how would they instantly know when a member was defeated?
Also i'd like to point out that even though Pain was using chakra, Naruto had to deal with 6 different bodies. SIX different bodies that can move simultaneously. He does not have the Byakugan where he can keep an eye on each one. He has Sage Mode that can sense chakra, but how is he going to sense chakra, when the bodies do not technically have chakra of their own? they use Nagatos from a building and this isnt DBZ, in Naruto...if your eyes are gone its game over. In DBZ if your eyes are unusable you can sense... or just blow up the damn planet and be done with it. Naruto had to deal with 6 different bodies with different abilities.
dealing with six bodies is not as difficult s u make it sound narutos kage bunshin have alwats been easily defeated because if he has 100 bunshins each one can only fight at 1/100 of the originals skill so each of these bodies only functioned at one sixth max potential (with maybe an exception to animal realm who fought with summons) and sensing nagatos chakra makes it easier for naruto because he only has to look for one scent, trail, tag w.e. u wanna call it so he would sense six different nagatos which is in my opinion easier than looking for six different chakras (unless ur karin)
this obviuosly does not directly apply to pein but in concept its the same he has to divide his chakra six ways and while naruto has all of his chakra in one source and its easier to get one body to respond the way u want it than it is six notice the realms reaction time increased as their numbers started dropping.
and im not taking from the fact that naruto has become extremely powerful he finished off four of the realms with relative ease and did so in amanner where they could not use the rinengan's security (aka he took advantage of the info given as all ninja should)
but my point is that fighting six bodies at 1/6 their potential is the same as fighting 1 person who is at 100% thats why naruto's clones havent really given him an advantage physically (instead clones and multiple bodies are used to mentally unnerve the opponent) in th end it all balances out because if u make 3 clone u and the clones will be at 1/3 of your potential so if somenone fought you and ur clones its the same as them fighting just u
and concerning zetstu he only watches what members and potential members do so he hasnt been watching naruto for 3 years a collective month is all the time id put into that theory (imo)