Why are you using Pain? Use Nagato instead. I don't think it's fair you're putting one part of Nagato in a fight. All of the Paths of Pain are basically parts of Nagato.
I'd say Nagato would win. Itachi second, and Neji Last. You said nothing about Dojutsu.
(I remember how buff/fast/strong Nagato was when he almost OHKO'd Bee and Naruto)
That means Itachi can read people's movements with Sharingan, and dodge them, and Nagato can use Rinnegan and OWN them. And Neji could use Byakugan to see through their clothes.
But besides that, Neji has Taijutsu swag. Nagato and Itachi have complete Dojutsu/Ninjutsu swag. You can't compare people with different swagger. You basically just took all of Nagato/Itachi's swag away saying they can't use Ninjutsu, and made them face the Fresh Prince of Taijutsu.
*You're doing this so people can recognize Neji didn't you? xD