He never had a serious fight and never showed his full power in his lifetime,so how can you say he can beat the top ninjas(Pein,Jiraiya,Minato etc)without this?
Well you also have to take into account that Pein, Jiraiya and Minato haven't fought at full power either, they didn't show all their jutsus and they were hype by Kage level ninjas such as A, Bee, Itachi, and Kisame. Pein master all 6 elements as a kid, did he use any of them? Nope. The black Jinton like jutsu Juubito used was all Rinnegan power, it created all jutsu and Nagato had the elements mastered as a kid so you're telling him he wouldn't be shooting off Lava, wood jutsu, magnetic force (Gaara's dad had this), Jinton or anything? He had 20+ years with the Rinnegan.
Jiraiya had other jutsus he haven't used, He had Earth and Fire jutsus but only used 1 earth jutsu and like 2-4 different fire jutsus, he also shown to be pretty skilled in seals. The only fight he was going all out was against Pein and even then he didn't use that many jutsus, he was fighting kage level ninjas while also trying to decode their secret and jutsus.
Minato have less screen time but more hype, arrogant Kages such as Oonoki and A even admit Minato's skills, Oonoki giving his ninjas flee on sight orders and A saying he thought no one would surpass Minato even though he always fought with Bee back then as tag team partners. Bee trembled at the mention of Minato when Naruto told him Minato created the Rasengan. We don't know Minato's Element (he was planning on adding it to Rasengan), Don't know if he had a second element, What other sealing jutsus did he have? Could he combine his elements for a KKG?
Nagato with his handicap only ever lost from Plot. Minato never lost (He beat Obito then used the Death Reaper Seal on Kurama before he was impaled by Kurama so he was already dying before that). Jiraiya Fought 3 kage level ninjas, killed them, got surprised attacked by a 4th, had to face all 6, got own, willed himself back alive, killed a 4th and then died. Jiraiya killed 4 Kage level ninjas in one fight, Itachi said him, Kisame and Jiraiya would all die or all be seriously injured if they fought, same result with backup. Jiraiya proved he could take on more than one Kage level ninja at once in my eyes.
This. If he has a chance against them while handicapped, what's stopping him from shitting on them while at full power in a fight to the death?
But then again, they didn't show all of their jutsus either as I described above so it doesn't really make that much of a differences since we don't know what Itachi healthy could do or what Pein, jiraiya and Minato can fully do.
He left because he was a Leaf informant on the inside as stated by Hiruzen, it was never his intention to claim Naruto nor fight any Konoha ninja, he was making his presence known to the elders of Konoha since Hiruzen died and ensured the protection of Sasuke. Him making his presence known was meant to intimidate the elders as well as Danzo so no harm would befall Sasuke.
Itachi told Kisame to kill Kakashi when he showed to have knowledge on Akatsuki and Gai saved Kakashi, this shocked Itachi as well so no he didn't sense him. Itachi was going to let Kisame cut off Naruto's legs to capture him so again that's a no. You're only remembering Itachi was a double agent but forgetting that he made a deal with Tobi and if he doesn't uphold that deal then all of Konoha is free games. He will sacrifice a few lives for the many, he did this with his clan in order to protect the whole village. Jiraiya is not part of Konoha, he left Konoha long ago, he choose to help Konoha but isn't duty bound like ninjas like Kakashi, Naruto, Gai, ect so killing him wouldn't matter much since he's barely in the village in the first place.
Itachi was a pacifist so he didn't like killing but did kill when he needed too. He tries to avoid fights when he can, even had Kisame fight the 4 tails Jinchuuriki himself.