Nagato wasn't in cotton during the fight, Kabuto assed direct control and doesn't have the experience or the know how on how nagato's abilities work as shown when the tried to use the second tsuchikage's abilities and failing because he didn't understand there draw backs fully. Nobody knows nagato's abilities better then Nagato.
they beat chibaku tensie then Boom Itachi got him they beat they
That's what you seem to not see. They beat chibaku tensie. Itachi didn't do it on his own. He couldn't. And once again Kabuto was in control.
Crippled Nagato is fasts to. He was able to dodge a rasenshurikan which at the time was the second or third fastest technique in the manga behind flying Thunder God and lighting augmented speed.
Itachi didn't have access to shusui' eye at the time, he gave it to Naruto and it was set to only activate when there was a threat to the village, (Sasuke). It's chi literally could only use it for one command (protect Konoha) Itachi literally explains that. Unless Nagato is about to destroy Konoha, then it's a non factor.
As a character Nagato was a confused boy that was given godlike powers that cost him the use of his body because he could not initially control it. he is raw power incarnate
You do know he was trained by Jiraya right? And was an incredibly competent ninja right? You also know that his greatest asset isn't his raw power but his versatility right?
Itachi is a precise ninja genius, with a plethora of some of the most broken techniques in the entire manga. He disabled nagato's summons, and as soon as he had an opening, one shot him. Thats what happened man. Also if you havent read the point I made about his Spirit Items, look for it plz.
All of his abilities have answers and ways to be defeated. You know that right? I know exactly how his sword and shield work. His shield is able to (from what we've seen) been able to block every Attack and works in a similar way to the truth seeking balls because they have all the chakra natures. We don't know if senjutsu would work, but it's a possibility (although it wouldn't be able to be exploited by Nagato considering he's not a sage)
And the sword instantly seals away whomsoever is stabbed by it. Let's not forget how draining chibaku tensie is and how much focus you have to put into it just so you can keep it going. That's probably the only reason Itachi was able to impale him with it. And also he had two jinchuuriki to worry about.
Your overestimating how powerful Itachi is...