Minato resorts to his Gama summon from Mount Myōboku; Gamabunta, Gamaken and Gamahiro are all tagged with a Jutsu-Shiki and given the time it takes Kisame to create that dome and fuse with Samehada it is entirely possible. This already counters the Waterdome argument as not only are the frogs versatile in water but Kisame can only trail one opponent at a time and Minato simply teleports to the toad which escapes it first. Sides the Space-Time barrier, it also provides a counter any wave-like attack given the
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to which Gamabunta can ascend and FTG; lastly it allows Namikaze to save the toads from any cornered situation. Kisame eventually or initially has his head removed by a kunai strike to the neck.
Side note: Samehada being sentient does not equate to it being knowledgeable of the methods to counter Genjutsu and therefore isn't an argument if Kisame is caught in the Frog Song.
Minato takes this due to intellectual and strategical advantage.
1 - Nothing suggests that Minato in his lifetime had the chakra reserves to summon three boss toads (although it's entirely possible, there's zero evidence to suggest this.) Plus he's fighting Kisame, so his chakra reserves are going to be chipped away at.
2 - Kisame can summon a shark or two to take care of Minato while he goes after Gamabunta. Minato won't be able to swim very fast underwater and he can't throw his FTG kunai due to being underwater.
3 - Minato will inevitably teleport back to Bunta when he starts to get overwhelmed by the sharks.
4 - Kisame finishes Bunta with GSB or 1000 sharks.
That's how the battle will realistically go. But in the case that Kisame somehow gets marked, this is what I see happening.
1 - Minato teleports to him, and stabs him with a kunai (he loses quite a bit of chakra too since he touched Kisame to mark him in the first place, and then touched him again after teleporting)
2 - Kisame heals and begins to counterattack. Minato quickly teleports away to safety.
3 - Minato teleports back (touching Kisame and losing chakra), tries again with a rasengan (thinking it will put him down) but the rasengan gets absorbed/tanked and Kisame counterattacks again, very possibly grabbing onto Minato (since he's expecting it and knows where the seal is placed on his body. Plus he is a sensor so he may be able to react to FTG just like Madara did with Tobirama.) Let's just say that Minato somehow teleports away again to safety. By now he is completely drained of chakra and even if he has any left, he may not have any breath left since this would be taking place underwater. Finishing Kisame is no easy task for Minato, and this is assuming that Minato miraculously tags him somehow.