The first part I agree with most of it. However his base skills are nothing but ordinary. Just look at how he matches up with other jounins in base.If I recall correctly, both the shadow clone technique are both jonin level techniques and his skills with them are better than anyone in the village ,and his chakra level in base mode far surpass any one in the village except maybe Tsunade and this is in base mode. The basis of many people ninjutsu depends on only a few niinjutsu, eg Minato whose ninjutsu was based on the rasengan and FTG
He also outsmarted Pain several times and whether he is in sage mode or not is irrelevant as it doesn't give you any sort of intelligence boost as far as I know. He has also done this several times. Please just give Naruto repect where it is due.
While he was fighting pein he was not using his base skills only sage mode skills. I don't recall much of that fight all I know is that he had massive help and already much intelligence.