First excuse me if it comes off that way, but i'm not really a Nagato fan. I simply thought about everything i've seen from both characters and stated my honest opinion.
Poster was right...100% healthy Nagato is pure fanfic(but so is any debate between how two characters would match up against each other in a non plot driven situation) and when i said Itachi's chakra capacity wasn't great...I was talking about his stamina/body also since part of chakra is derived from the cells/physical energy in the body...ie stamina but living Itachi was sick
Now as for Kabuto controlling Nagato being the same as Nagato fighting himself...well I'll have to go back and reread but i distinctly remember kabuto saying he wouldn't control Diedara because he didn't understand his art...i took this as him not being able to use Diedara's justu as effectively as the original.(And at one point in the fight from a comment he made it seems that Kabuto was so focused on the jinchuuriki that he forgot Itachi's presence...but this is up for interpretation. Also the fact Kabuto was only going for a capture even on edo Itachi so)
though it does seem Naruto and Bee where dumb down during this fight...both can make more than one chakra limb and neither used it to free themselves from Nagato.
As for Naruto's full speed...it doesn't appear that he used it to me, though maybe he couldn't control it fully without concentrating...A lot of people say his Kyuubi chakra mode's speed is exaggerated/slow because Itachi kept up with it and say how Itachi Dominated the Jinchuuriki in that clash...but the only time i saw itachi engaged with Naruto was when he was falling from the sky after he jumped and Naruto stood there and blocked his strikes as he was coming down(Does just this give him Naruto's speed) and it seemed like Bee handled himself well against Itachi driving him back with kenjutsu
I can't say for sure, but going by Rasenshuriken(a large building destroyer at most) and Bijuu dama(Mountain buster) i doubt their three attacks were on the same level...I believe they just used the strongest projectile attacks available to them.(though looks like bee might have held back a lot on that Tbb)
Ignore the sound based genjutsu(I had a bad fan translation)