Since Samehada isn't restricted, Kisame wins without much of any effort. Aquatic Shock-wave throws all FTG Kunais back and merging with the sword also grants him the ability to become a class one tracking-sensor. His body has enough durability to tank Rasangan. Any damage is healed because of Samehada. Shark Missle ends Minato. Low difference. Restrict the sword and I still give this to Kisame Mid-difference. His chakra reserves are far too large to even be out-classed by the likes of Minato.
Minato can sadly win. S/T barrier in the water dome as Kisamehada flies at him, or the GSB. Hell, even in a normal submerged environment to suck some of the water away.
^ I dislike his characterization. Anyhow, I hardly see anything in Minato's arsenal that even harms Kisame to tilt this battle even slightly in his favour.