Minato wins.
Minato could actually kill him before he performs any techniques, people seem to forget the fact that to use water techs, one has to form a number of seals whereas Minato is an incredibly fast ninja who simply has to get a kunai close to an individual, so basically as Minato has to do is get himself within 5 feet of Kisame, something he can do relatively easily by running at Kisame with the same speed he used to catch baby Naruto and run up a wall before Tobi could make contact. On getting that close he simply needs to put a kunai near Kisame and he can teleport anywhere around him and kill him.
People also forget the fact that for Kisame to regenerate major injuries, Samehada has to fight absorb bijuu levels of chakra from someone. There's no bijuu in this fight so Kisame can't absorb and heal the injuries Minato will inflict on him.
Now let's say Kisame gets the chance that scores of ninja who faced Minato didn't get and actually forms the seals for his techniques, he can't use the water bubble he used against Bee here. Why? Because he had to first absorb bijuu levels of chakra from Bee to perform it. There's no bijuu here so that technique can't be used. Now as for Kisame's other techniques, he can create a lake to flood the battlefield making kunai use for teleportation difficult. However this battle is in the woods so even with water everywhere covering the earth, Minato can mark surrounding trees which won't be so easily washed away and to combat Kisame's large ninjutsu, can summon Gamabunta whose body mass is the same as Kisame's largest techniques. Gamabunta's Water Gun technique is as big as most of Kisame's techniques, the toad is big enough to counter Kisame's thousand feeding sharks by merely sitting on them or slicng them with his sword. He can also use massive oil bullets which can immobilise Kisame for Minato to kill him or Minato can simply ignite the oil with simple explosive notes for massive explosions. Databooks also mention that toads in Myobokuzan are skilled in MANY sound based genjutsu so Kisame is in real trouble here since he(like Naruto who was unable to break finger genjutsu) has a 2/5 in genjutsu. Minato has every advantage.
