Nagato has shown that he has the ability to put mental block, has shown to have buakygun capabilities, and when kakashi MS looked upon the renningun everything went pitch black and the renningun was shacking. Also since we have not seen the Renningun been put under any Visual genjutsu, any genjutsu for now is a NO.
Amutrasu can be predicted and Nagato has the abilities to repeal it. Since we have not seen Nagato absorbing the Flames we can Say it can't for now, However by using the tech too manipulate gravity it well back fire and hit Itachi, even if the flames doesn't hit Itachi the tech would have injured him or moved him far away.
Susunno is slow however very powerful, but because it is made by pure chakra it can be absorbed, also it can't stand the Almighty push, Planetary devastation.
If Nagato is a cripple that means itachi is some what blind and very sick, also Itachi has low Chakra while Nagato has a lot. Nagato can use most of his powers at the same time.
It does not matter who is smarter than who, although i do agree that it plays a big part that does not mean Itachi well win. Another thing is that Itachi has the Mirror tech however it has not been proven that it can repal the abilities that Nagato has.
Ask your self this question can Itachi take on a six tailed Naruto with only one tech.....
Like i stated before Nagato has this with mid diff
Genjutsu will work on Nagato. Mental blocks can only obstruct people who try to go into Nagato's mind, and are unable to protect him from Genjutsu. If they could protect him, why was he affected by the sound genjutsu used by Ma and Pa? Also, it remains to be seen if Nagato can put mental blocks on his mind while he is still alive.
Amaterasu is useless, yeah.
Susanoo can be absorbed? well, I disagree on this one. Susano'o may be made of pure chakra, but it also has living tissues, bones and a solid armor.I've never seen Nagato absorbing solid objects using his preta path, and so i'll have to disagree.
Susanoo can protect Itachi from most of Nagato's offensive techniques( like asura path's weapons and other elemental techniques), and so can his Yata no Kagami. Totsuka can seal Nagato if it hits him.
Itachi is much smarter than Nagato, but Nagato has too many godly techniques.
Conclusion:
1. Nagato will win with high difficulty( He'll probably be forced to use CT).
2. Itachi has a small chance of winning if he puts Nagato under genjutsu and seals him off before he can break out of it.