Itachi could win due to ;
Tsukuyomi hitting Minato ; while Minato could be ''efficient'' in dealing with genjutsu, Tsukuyomi put Kakashi down on his knees while his Sharingan had the natural ability to provide him some protection, yet even with this, Itachi held back to prevent killing him.
Itachi is the best kunai user of the manga, and also was praised so far as having the fastest hands. If there is one person who could neutralise FTG, its him because he has the sharingan, the hand speed and precision to counter kunais as well as the intellectual capabilities to understand anything in an instant.
Minato could win due to ;
the fact that his way of fighting seems pretty efficient in terms of chakra usage. FTG doesnt seem to consume that much chakra, although it takes a lot of chakra control which Minato has. This could give him the edge as Itachi could be force to use Susano for a long period of time, and this could put him in pain and use his chakra in the long run (even if its only a baby Susano which should be enough to tank the rasengan)
In All honesty, this match up is pretty much impossible to debate, because both of them have imo an equal chance of winning.
If Minato doesnt avoid genjutsu he is done for as even if he were to survive it, the side effects would be enough to prevent Minato from either moving as fast as he would normally do, or it would prevent him from using his chakra with high efficiency.
if Minato is able to avoid genjutsu then Itachi is forced to try and hit Minato with something else... and with MInato's speed, there isnt much Itachi would be able to throw at him that he wouldnt be able to avoid. The only thing that could happen really is Itachi fooling Minato to hit a crow exploding bunshin or something.
To me Minato and Itachi are simply equals.
Equally strong, equally smart, equally bad asses, both died young, both were unrivaled AND young prodigies and reached a height that was only reached legitly by one man ; Hashirama. Itachi and Minato didnt have Rinnegan, EMS, a Bijuu or Senju DNA given to them, and they made it to the top (top 10 imo) despite being much younger than anyone else.
