To be totally honest, the fact that Kabuto was controlling him doesn't even affect the results of the fight. You say that Nagato had no interest in hurting them, but Kabuto was controlling Nagato and knows all of his techs. Kabuto controlled Nagato very well and isn't stupid. He knew of all of his techs. It was the same as if Nagato wanted to hurt them himself. Itachi got too far away from Nagato when he was freed from the Edo Tensei, so Kabuto didn't make Nagato use soul rip, Itachi was out of range. Itachi's problem when he was alive wasn't low chakra levels. He has a bigger chakra pool than Hebi Sasuke, even while being sick. His problem is low stamina due to being sick. The claim that ocular genjutsu doesn't work on rinnegan was already discredited. Zetsu proved the whole "superior dojutsu is immune to lower dojutsu techs" when he stated that 3-tomoe Sasuke had a chance at genjutsuing MS Itachi. Nagato has no answer to Tsukiyomi or Kotoamatsukami. However, Itachi did not use those techs, because they would have been useless at the moment, considering that Kabuto was completely controlling Nagato at the time, Nagato's mind was not there at the moment. As an Edo, Itachi could have spammed Yasaka Magatama 2 more times and taken out the Chibaku Tensei himself, if Bee and Naruto were not there & he didn't have a chitchat with them. You say that Edo Itachi was brought to Edo Nagato's level because Nagato was crippled, however, Nagato was always crippled ever since the age of 16 from saving Konan from Hanzo's attack. That wasn't anything new, non-crippled Nagato in his prime doesn't exist and is fanfic due to that, considering he was injured well before he reached his prime.
Just as Itachi may not have counters for some of Nagato's rinnegan techs, Nagato has absolutely no counters to Itachi's higher level genjutsu. Also, you stated that the only way Nagato is losing is if he doesn't have intel on Itachi. 90% of the fights in the Naruverse occur with neither side having intel, just like Edo Nagato vs Edo Itachi did. Actually, Itachi didn't really know anything about rinnegan techs and Nagato knew more about MS, considering he knew what amaterasu was. Kakashi knew Itachi used genjutsu and had MS, but still looked into his eyes for the hell of it. Orochimaru even with intel attacked a 14 year old Itachi, full knowing what he could do. That's why he wanted to take over Itachi, he knew his strength and the possibilities with the sharingan. But he got one-shotted by Itachi and Itachi didn't even make eye-contact w/ him, he just activated his 3-tomoe and Oro looked at his back and it was paralysis genjutsu gg. Where do you think Kabuto got the majority of his info about Edo Itachi? That was all from Oro. lol