Sorry guys this is long, read if you have the patience.
1) Naruto Vs Pain: It was just opinion of zetsu that Naruto was stronger than sasuke at that time, not fact. it was based on the premise that Pain was the strongest, and whoever takes down the biggest guy in the block becomes the new king. We all watched the fight, one of them had to go down, and it had to be Pain. Naruto would have been a goner if it wasn't for intel, kyuubi rampage, Minato stepping in, and the dialogue with nagato culminating in suicide. I'm pretty sure naruto couldn't kill the real nagato (not the pains) at his level then. Nagato was also at a major disadvantage. Sick, immobile, Time lag controlling the pains, etc pretty sure he could use all rinnegan abilities from his chair. Bottom line is, they had to put nagato at a disadvantage for naruto to emerge as the winner.
At this time also, naruto couldn't control kyubi, he was said to have mastered sage mode, but we all know he just mastered control (not turning into a frog) and surpassing jiraiya. Except for frog kumite, chakra sensing, a little bit of speed boost, and sheer strength most of which he doesnt use creatively, He didn't come close to what we know sage chakra is capable of.
2) Sauke Vs Itachi: Itachi could have killed sasuke. It was all part of his plan to die by sasuke's hand as his own redemption. The fight was also an opportunity for him to see how far sasuke has come. He wanted a worthy opponent, who else was on the opposing side but sasuke?. He planned to die but he wasn't gonna just let sasuke stab him to death in one attack after putting him through so much to motivate him to get stronger.
3) Naruto vs sasuke final: Sasuke couldn't kill Naruto, period. He did all he could and was even frustrated at his failure. Can naruto kill sasuke? We don't know, all we know is he fought defensively with the same techniques he uses for attack, just a different motive. He had to use his best skills to counter sasuke's best attacks and they always nullified eachother, so maybe sasuke could also nullify naruto's best attacks in the same manner.
I would say both are equal overall. They both have their stronger sides. Sasuke has more cognitive abilities than Naruto and is able to efficiently utilize his powers in battle. Naruto on the other hand has abilities he can't utilize efficiently and only goes into strategy mode when he's about to get killed. His default is perseverance and brute force. Both of them operating at these two modes will always be equal.
We keep comparing them based on what we know they can do (subjectively) and not based on how they were created (objectively).
If naruto had IQ like the smart guys in the series (itachi, sasuke, 1-4th hokages, kabuto, kakashi, shikamaru, oro), then that would be a different case, but he clearly doesn't. Naruto is also inconsistent with his abilities. Today he's faster than Minato, tomorrow he's as slow as **** even in the same mode.
We've seen susaano bypassed a couple of times with sound genjutsu (kabuto), undeground attacks (gaara with sand) and danzo's wind sucking monster. Naruto can pull off 2 of these (sound genjutsu with sage toads which will take out the susaano user immediately.) and kyuubi chakra attacking from underground. But he will prefer to take down susaano with nukes or sheer strength. He can confortably merge with the sage toads now while protecting them with his chakra cloak enhancing his battle abilities.
In summary, Naruto's only limit is in how much he can discover what is available to him, strategise and use it creatively at genius level. Only then will he truly trump Sasuke. So far he has all it takes to defend against sasuke and also possesses the strongest and unique forms of raw chakra, and we have seen what the geniuses can do with these chakra types.
