I wanted to do a breakdown of the chakra-related skills that Naruto has learned over the series - excluding Kurama Mode and Six Paths Sage Mode - to get some perspective on his aptitude for the ninja arts.
Naruto’s Chakra
For context, Naruto has always had massive chakra levels because of the Nine-Tails’ chakra mixing with his own all his life (and likely because he’s an Uzumaki too) but the Nine-Tails also made controlling his chakra more difficult and that poor chakra control made using jutsu harder.
Ebisu explained that Naruto’s problem was twofold; he’s bad at moulding chakra so he always creates more chakra than he needs and he’s bad at controlling chakra so he can only use a small portion of what he creates. This makes it difficult for him to use the right amount of chakra for activating his jutsu.
Clone Jutsu (E-rank ninjutsu)
Naruto was only able to create one poorly-made clone for the Academy’s Final Exam when the requirements to pass were to create three clones. Like Ebisu said, he doesn’t apply enough chakra to the Clone Jutsu which prevents him from making even a single stable clone.
Every other student in his class was able to pass the same exam while he had failed that exam twice before as well.
Naruto is never shown attempting the Clone Jutsu again.
Transformation Jutsu (E-rank ninjutsu)
Naruto was able to use the Transformation Jutsu successfully by the time he graduated, often using it to transform into a naked woman.
But before that, he couldn’t use this jutsu properly after three years at the Academy which surprised his teacher and was considered ridiculous by his peers, telling us that he spent an unusually long time trying to learn it.
Body Replacement Jutsu (E-rank ninjutsu)
Naruto used this jutsu once in the Land of Waves Arc. It is one of the jutsu taught at the Academy but he is never shown using it again.
Shadow Clone Jutsu/Multiple Shadow Clone Jutsu (B-rank ninjutsu/A-rank kinjutsu)
Naruto was able to successfully perform this jutsu after learning it from the Forbidden Scroll of Seals with approximately 12 hours of hard work.
Considering Naruto has struggled with lower-ranked jutsu for much longer either a) this ninjutsu requires little-to-no chakra control to justify Naruto’s success and its ranking is purely because of the chakra cost while otherwise being incredibly easy to learn or b) Naruto has an unusually strong affinity for this particular ninjutsu.
Tree Climbing
Kakashi taught Naruto, Sasuke and Sakura the tree climbing exercise during the Land of Waves mission.
Naruto applied too little chakra which prevented him from adhering to the tree like Ebisu later describes. He initially failed to improve much until he got advice from Sakura and started to catch up to Sasuke.
Then after hearing about Kaiza, Naruto spent each night training by himself (unlike Sasuke) up until the last day of training where they reach the top of the tree together.
Water Walking
Ebisu taught Naruto the water walking exercise where he got the knack of the exercise faster than expected while under the influence of Orochimaru’s seal. Once unsealed, Naruto was able to stand on the water but couldn’t maintain it for long. This is the last of the training that we see but Jiraiya presumably got him to exhaust his chakra each day and Naruto could easily walk on water during his battle with Sasuke.
Even so, three weeks later, Jiraiya still considered Naruto to have poor chakra control.
Summoning Jutsu (C-rank ninjutsu)
Jiraiya taught Naruto the Summoning Jutsu but he didn’t show much aptitude for it and made little progress after 21 days of non-stop training.
It was a means to an end as Jiraiya wanted him to tap into the Nine-Tails’ chakra by releasing as much chakra as possible; the Summoning Jutsu was ideal for this as the more chakra used then the greater the summon. Naruto only being able to summon tadpoles ties into Ebisu’s explanation that he doesn’t apply enough chakra to his jutsu.
When the Nine-Tails gave him chakra, he successfully summoned Gamabunta. Naruto spent the next three days unconscious and fought in the finals the following day.
The next time he performed the Summoning Jutsu, he accidentally summoned Gamakichi. Then he finally summoned Gamabunta by using the Nine-Tails’ chakra again.
He tried to use the Nine-Tails to summon against Itachi and Kisame but he was stopped so it is unknown if he would have succeeded.
Naruto’s next and last attempt in Part 1 only summoned Gamatatsu, showing no more improvement from when he fought Gaara.
In Part 2, Naruto successfully performed the jutsu both times as he summoned Gamahiro for the Food Cart Destroyer Jutsu and the matured Gamakichi against the Ten-Tails.
Rasengan (A-rank ninjutsu)
Naruto completed the first stage in three days and one night. He figured out how his chakra needed to move to burst the water balloon (thanks to a cat) but because he didn't have the necessary chakra control, he improvised by using another hand.
He completed the second stage in three weeks or so. The next day(?), Jiraiya gave him a hint to improve his focus which allowed him to finally complete it.
And the third stage was completed seven days later to win his bet with Tsunade. Once again, Naruto didn't have the control to focus his chakra the correct way despite his continuous efforts. It wasn't until he came up with another improvised method by using a shadow clone to focus the chakra that he was able to complete the final stage.
Approximately four years later - after achieving Six Paths Sage Mode - Naruto was able to use the Rasengan without needing shadow clones, senjutsu or the Nine-Tails.
Big Ball Rasengan (A-rank ninjutsu)
During the two-and-a-half years training trip, Naruto created the Big Ball Rasengan using the Nine-Tails’ chakra. Over a year later, he was able to create a much larger version without needing the Nine-Tails’ chakra.
Genjutsu Release
During the two-and-a-half years training trip, Naruto learned how to break genjutsu but was unable to use this successfully against Itachi and required outside assistance.. He was later caught in another genjutsu by Itachi and made no attempt to release it.
Wind Release: Rasenshuriken (S-rank ninjutsu)
Naruto spent two days learning nature transformation for the wind chakra nature. This normally takes years but Naruto used the shadow clone training method (and Asuma’s advice) to cut the leaf and then the waterfall abnormally fast.
He then spent approximately seven days creating the Rasenshuriken with the shadow clone training method.
Using 200 clones, he spent one day training in pairs. After Kakashi’s advice, Naruto spent another six days training in groups of three before the confrontation with Hidan and Kakuzu. Naruto was first only able to create “Wind Release: Rasengan” but could later create Wind Release: Rasenshuriken though it only worked half the time.
It is unknown whether Naruto continued training the Rasenshuriken due to the consequences, the following hunt for Itachi immediately followed by Jiraiya’s death.
He completed the jutsu once he learned Sage Mode and approximately three years later - after achieving Six Paths Sage Mode - Naruto could use the completed version without any assistance.
Senjutsu
Naruto spent more than a day but less than a week learning Sage Mode.
(Based on the Animal Path’s autopsy which would have taken a week or less to complete and was still underway when Pain attacked and Naruto returned to Konoha.)
It ordinarily takes time to learn - it's unknown what the average length of time is - but using the toad oil is a shortcut to speed things up. Naruto tried to shorten this process even further using shadow clones but it was too difficult and he quickly went back to training by himself.
Fukasaku considered Naruto quicker on the uptake than Jiraiya (implying he also used toad oil) and was impressed with his progress when he stopped using the oil. Since Naruto achieved Sage Mode without any frog aspects, he thought that Naruto might have had the potential to become a greater sage than Jiraiya.
Immediately after this, Fukasaku taught Naruto the Frog Kata in time to fight Pain in Konoha.
Naruto continued to improve his Sage Mode’s duration and how quickly he could enter that state though he eventually received the superior Six Paths Sage Mode in the Fourth Shinobi World War.
Naruto’s Chakra
For context, Naruto has always had massive chakra levels because of the Nine-Tails’ chakra mixing with his own all his life (and likely because he’s an Uzumaki too) but the Nine-Tails also made controlling his chakra more difficult and that poor chakra control made using jutsu harder.
Ebisu explained that Naruto’s problem was twofold; he’s bad at moulding chakra so he always creates more chakra than he needs and he’s bad at controlling chakra so he can only use a small portion of what he creates. This makes it difficult for him to use the right amount of chakra for activating his jutsu.
Clone Jutsu (E-rank ninjutsu)
Naruto was only able to create one poorly-made clone for the Academy’s Final Exam when the requirements to pass were to create three clones. Like Ebisu said, he doesn’t apply enough chakra to the Clone Jutsu which prevents him from making even a single stable clone.
Every other student in his class was able to pass the same exam while he had failed that exam twice before as well.
Naruto is never shown attempting the Clone Jutsu again.
Transformation Jutsu (E-rank ninjutsu)
Naruto was able to use the Transformation Jutsu successfully by the time he graduated, often using it to transform into a naked woman.
But before that, he couldn’t use this jutsu properly after three years at the Academy which surprised his teacher and was considered ridiculous by his peers, telling us that he spent an unusually long time trying to learn it.
Body Replacement Jutsu (E-rank ninjutsu)
Naruto used this jutsu once in the Land of Waves Arc. It is one of the jutsu taught at the Academy but he is never shown using it again.
Shadow Clone Jutsu/Multiple Shadow Clone Jutsu (B-rank ninjutsu/A-rank kinjutsu)
Naruto was able to successfully perform this jutsu after learning it from the Forbidden Scroll of Seals with approximately 12 hours of hard work.
Considering Naruto has struggled with lower-ranked jutsu for much longer either a) this ninjutsu requires little-to-no chakra control to justify Naruto’s success and its ranking is purely because of the chakra cost while otherwise being incredibly easy to learn or b) Naruto has an unusually strong affinity for this particular ninjutsu.
Tree Climbing
Kakashi taught Naruto, Sasuke and Sakura the tree climbing exercise during the Land of Waves mission.
Naruto applied too little chakra which prevented him from adhering to the tree like Ebisu later describes. He initially failed to improve much until he got advice from Sakura and started to catch up to Sasuke.
Then after hearing about Kaiza, Naruto spent each night training by himself (unlike Sasuke) up until the last day of training where they reach the top of the tree together.
Water Walking
Ebisu taught Naruto the water walking exercise where he got the knack of the exercise faster than expected while under the influence of Orochimaru’s seal. Once unsealed, Naruto was able to stand on the water but couldn’t maintain it for long. This is the last of the training that we see but Jiraiya presumably got him to exhaust his chakra each day and Naruto could easily walk on water during his battle with Sasuke.
Even so, three weeks later, Jiraiya still considered Naruto to have poor chakra control.
Summoning Jutsu (C-rank ninjutsu)
Jiraiya taught Naruto the Summoning Jutsu but he didn’t show much aptitude for it and made little progress after 21 days of non-stop training.
It was a means to an end as Jiraiya wanted him to tap into the Nine-Tails’ chakra by releasing as much chakra as possible; the Summoning Jutsu was ideal for this as the more chakra used then the greater the summon. Naruto only being able to summon tadpoles ties into Ebisu’s explanation that he doesn’t apply enough chakra to his jutsu.
When the Nine-Tails gave him chakra, he successfully summoned Gamabunta. Naruto spent the next three days unconscious and fought in the finals the following day.
The next time he performed the Summoning Jutsu, he accidentally summoned Gamakichi. Then he finally summoned Gamabunta by using the Nine-Tails’ chakra again.
He tried to use the Nine-Tails to summon against Itachi and Kisame but he was stopped so it is unknown if he would have succeeded.
Naruto’s next and last attempt in Part 1 only summoned Gamatatsu, showing no more improvement from when he fought Gaara.
In Part 2, Naruto successfully performed the jutsu both times as he summoned Gamahiro for the Food Cart Destroyer Jutsu and the matured Gamakichi against the Ten-Tails.
Rasengan (A-rank ninjutsu)
Naruto completed the first stage in three days and one night. He figured out how his chakra needed to move to burst the water balloon (thanks to a cat) but because he didn't have the necessary chakra control, he improvised by using another hand.
He completed the second stage in three weeks or so. The next day(?), Jiraiya gave him a hint to improve his focus which allowed him to finally complete it.
And the third stage was completed seven days later to win his bet with Tsunade. Once again, Naruto didn't have the control to focus his chakra the correct way despite his continuous efforts. It wasn't until he came up with another improvised method by using a shadow clone to focus the chakra that he was able to complete the final stage.
Approximately four years later - after achieving Six Paths Sage Mode - Naruto was able to use the Rasengan without needing shadow clones, senjutsu or the Nine-Tails.
Big Ball Rasengan (A-rank ninjutsu)
During the two-and-a-half years training trip, Naruto created the Big Ball Rasengan using the Nine-Tails’ chakra. Over a year later, he was able to create a much larger version without needing the Nine-Tails’ chakra.
Genjutsu Release
During the two-and-a-half years training trip, Naruto learned how to break genjutsu but was unable to use this successfully against Itachi and required outside assistance.. He was later caught in another genjutsu by Itachi and made no attempt to release it.
Wind Release: Rasenshuriken (S-rank ninjutsu)
Naruto spent two days learning nature transformation for the wind chakra nature. This normally takes years but Naruto used the shadow clone training method (and Asuma’s advice) to cut the leaf and then the waterfall abnormally fast.
He then spent approximately seven days creating the Rasenshuriken with the shadow clone training method.
Using 200 clones, he spent one day training in pairs. After Kakashi’s advice, Naruto spent another six days training in groups of three before the confrontation with Hidan and Kakuzu. Naruto was first only able to create “Wind Release: Rasengan” but could later create Wind Release: Rasenshuriken though it only worked half the time.
It is unknown whether Naruto continued training the Rasenshuriken due to the consequences, the following hunt for Itachi immediately followed by Jiraiya’s death.
He completed the jutsu once he learned Sage Mode and approximately three years later - after achieving Six Paths Sage Mode - Naruto could use the completed version without any assistance.
Senjutsu
Naruto spent more than a day but less than a week learning Sage Mode.
(Based on the Animal Path’s autopsy which would have taken a week or less to complete and was still underway when Pain attacked and Naruto returned to Konoha.)
It ordinarily takes time to learn - it's unknown what the average length of time is - but using the toad oil is a shortcut to speed things up. Naruto tried to shorten this process even further using shadow clones but it was too difficult and he quickly went back to training by himself.
Fukasaku considered Naruto quicker on the uptake than Jiraiya (implying he also used toad oil) and was impressed with his progress when he stopped using the oil. Since Naruto achieved Sage Mode without any frog aspects, he thought that Naruto might have had the potential to become a greater sage than Jiraiya.
Immediately after this, Fukasaku taught Naruto the Frog Kata in time to fight Pain in Konoha.
Naruto continued to improve his Sage Mode’s duration and how quickly he could enter that state though he eventually received the superior Six Paths Sage Mode in the Fourth Shinobi World War.