Well jarayias sage mode would protect him from itachis genjutsu. He would however have problems with itachis susanoo. But ultimately I feel as though jarayia would win this because he has a wider range arsenal. Plus itachi has already admitted to being equal or even less than jarayia. Because when he said that comment about they would both die he was also considering the fact that kisame was there. So I say one v one jarayia takes it. I Mean if you think about it if jarayia knew about the paths I think he could have taken out Nagato himself