compare Itachi's childhood with nagato's childhood to begin with. Itachi's way of doing things was far more advanced than anyone. Everyone in konoha and uchiha clan respected Itachi and called him a genius. Not because he had all the jutsus available to him. Not because he was able to awaken the sharingan at young age. Everyone is able to awaken sharingan if they put effort into doing it. It doesn't take a genius to awaken a sharingan. Itachi's leadership, way of behavior, thinking and the way he analyzes things is extremely good. At young age, he looked more matured than anyone else. He was taking care of sasuke when he was probably just five to six years old. At young age he looked calm and dangerous.
Nagato in the other hand, you can tell from his childhood. He was responsible for his parents death for creating a noise while trying to scape from those konoha ninjas. Nagato at young age was a cry baby. Maybe the word crybaby is a little too hard to say but Yahiko even called him a crybaby. He would always stay crying rather than to stay calm. He lacks leadership and in order to be a leader, you need to be able to make decisions and be smart. Yahiko was doing almost everything for him while he was hiding behind him. For example, when konan got kidnapped by Hanzou, Nagato couldn't think of anything. Yahiko had to make a decision for him. He lacks intelligence.
Trust me, kabuto controlling Nagato is a plus. Kabuto in a way is smart. Thus, the reason why Kabuto stayed alive for such a long time. Kabuto even made madara to accept him to help him with the war. Madara even acknowledges him. I don't think it would have been any different if nagato wasn't being controlled by kabuto.
Once again, A LOT OF PEOPLE make this mistake of thinking that just because you the most powerful attacks you are going to win. It's not like this at least not in naruto. Minato was able to defeat Madara with two jutsus. Rasengan and FTG. Madara was able to make his body intangible, teleport and take people to other dimension but he was defeated by Minato because minato came up with a strategy far superior than madara. Minato studied madara first until he found what he was relying most at. Madara was trying to touch Minato so that he can send minato to another dimension. This was Madara's goal. Minato found out about this and came up with a counter strategy. Afterwards in a matter of seconds Minato came to be victorious.
Naruto is able to teleport away like yondaime minato but he doesn't have the mental intelligence of his father to be able to come up with strategies and make the best of his powers.
Bee, rushes nagato like a fool thinking that with his transformed form would beat nagato. Bee rushes without thinking and he almost dies.
This is what seperates Itachi and Minato from the rest. Their ability to make the best of their techniques. They don't have to be extremely strong techniques but they can get the best of them and they can THINK and find weakness of the opponents and stay ten steps ahead of them.
