Itachi would win because I don't see Kisame having a counter for amaterasu. He does have samehada but I doubt it can absorb all the flames. On top of this, Itachi is smarter, faster (hand seals and foot speed).
Saying all this I believe Kisame will give him a good fight. This is because he is Itachi's partner so he will know Itachi's tricks. Also Kisame is a sensor when fused with samehada so he can fight Itachi without looking into his eyes. Also samehada can break Kisame out of genjutsu. Kisame can also suck up the chakra from Itachi's susanoo and drown Itachi in a giant water dome.
Itachi would be forced to use amaterasu on Kisame which will take a toll on Itachi but it will grant him victory in the end. All of Itachi's other jutsus will be relatively ineffective against Kisame because of his monstrous healing abilities and chakra absorption.
Overall Itachi wins mid-high difficulty.