That would be a tough fight.
Both characters use different jutsus, but thye generally do the same damage. Let's analyse the jutsus.
Kakashi:
Sharingan/MS - Predict enemy movements + Kamui
Raikiri - Good against Kisame's water style.
Intelligence - Smart, usually have good strategists.
Kisame:
Samehada - His trump card. A big sword, able to absorb chakra, transfer chakra to owner and heal him. Also able to merge with Kisame to increase his power.
Incredible chakra - He has a lot of chakra, although most of the credit goes to his Samehada for providing it.
Kakashi + teammates (to carry out strategists) = kakashi's victory
Kisame + Samehada = Kisame's victory
So if Kakashi goes 1 on 1 with Kisame.. I'd say Kisame may win , but barely.