Honestly, I've seen both debates, and I see Minato with the upper hand. What do we know about him? He is incredibly intelligent. He was the HOKAGE. What does this mean? He knows about the Uchiha's prowess with genjutsu. Now, the main argument for this is "well, then why did he look in Tobi's eyes???". The answer is simple. Minato knew that Tobi was already using genjutsu on the fox. That by itself would take up a LOT of his concentration. So Tobi, because he was using genjutsu on the fox, would be unable to use it on Minato. Minato knew this, and freely looked at Tobi. So otherwise, considering Minato's knowledge, he would most likely not look in Itachi's eyes.
Added to the genjutsu argument is Minato's speed. If Minato is faster that the Raikage, and the Raikage could avoid Sasuke's MS focusing on him, Minato should also be able to avoid Itachi's focusing on him with his sharingan. This also puts genjutsu out of the question. Similarly, the same argument will obviously be used for Minato's ability to avoid Amaterasu.
So the last obstacle is Susanoo. I'm sure you've heard of the FTG radius argument. The truth is, in the end, that it would work. Even if Itachi deflects all of Minato's kunai (which he may have more of that Itachi has shuriken to deflect with) Itachi would be unable to predict where Minato teleports to. Minato could place seals on the ground getting closer and closer to Itachi, all the while using his speed to avoid genjutsu and Amaterasu, and also forcing Itachi to keep up Susanoo. This on its own basically dictates that Minato would outlast Itachi, because Itachi NEEDS to keep up Susanoo against Minato. Regardless of his 5 in speed in the data book, Minato is far faster, and would crush Itachi if Itachi attempted to conserve chakra by dropping Susanoo. So eventually, Minato would get close enough to teleport into Susanoo using the radius of FTG.
Another even more plausible way for Minato to win is to use the S/T barrier. Using this ability, Minato can warp projectiles wherever he wants, even inside of Itachi's Susanoo. That alone gives Minato the upper edge.
I will not deny that Itahi COULD win. But Minato would win the majority of the time. It would however, be very close. I have it at about 55-60/100 in Minato's favor.