Okay Negative I promised you I would post in this thread supporting Kisame. Now that I read your entire thread, it does seem like it would be a very close fight that could go either way high difficulty. Nevertheless, I still think Kisame would win.
Well let's start correcting the fallacy that raiton>suiton. Remember when Mei used her water dragon jutsu which the Raikage electrified? It did not electrocute Mei in anyway so I doubt Kisame would be fried. Also samehada should have no trouble absorbing gian as I don't think it is an attack with too much chakra nor is it a fire release attack.
Also I highly disagree when you said that Kakuzu is immune to wind techniques. He is immune to earth based and physical attacks but he is only somewhat resistant to wind techniques. Wind has a high power of slicing and top tier wind users will be able to get through doton domu IMO just like Naruto did with FRS.
Anyway I'm quite sure that Kisame water attacks will douse any and all of Kakuzu's flames. Kisame won't get overwhelmed by Kakuzu's fire attack because Yamato and Naruto were able to dispel the flames and I think Kisame, being the most powerful suiton user in the manga won't get overwhelmed. This will mean that Kakuzu won't be able to overwhelm Kisame because Kakuzu's raiton is absorbed and the katon/fuuton combo is countered by a more powerful suiton.
As for the earth grudge threads, well I think that would be problematic but Kisame could use samehada to cut them up as he is a top tier swordsman. Kisame also has super human strength so he should be able to break them before Kakuzu manages to steal a heart.
I must admit that Kisame has absolutely nothing on doton domu but it isn't like Kakuzu can maintain the jutsu forever. It requires Kakuzu to use a constant amount of chakra so eventually, Kakuzu's chakra supplies will diminish allowing Kisame to finish him off. Although this will be a long fought battle since Kakuzu is a stamina beast and didn't show any signs of exhaustion unlike Kakashi and Shikamaru who became exhausted quite easily despite the fact that Kakuzu's ninjutsu seems more chakra taxing to me.
I think Kisame has better taijutsu compared to Kakuzu but neither will be able to do a significant amount of damage against the other because of doton domu and samehada regeneration. However, a CQC bout will only favour Kisame because he will be able to absorb Kakuzu's chakra.
Kisame's wide AoE attacks should allow him to attack multiple hearts at once as well as counter the massive elemental blasts from Kakuzu especially if samehada weakens Kakuzu's techniques.
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Kisame's
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technique will allow his attack to become stronger and stronger as it absorbs the opponents ninjutsu thereby allowing his own attack to use the power of Kakuzu's attack and divert the full force against his own opponent.
You make a good point that is was especially hard for Kakashi to take down Kakuzu's hearts on his own but this is because Kakashi is a lot weaker than Kisame, especially during that arc.
Still if Kakuzu manages to steal Kisame's heart, Kisame won't be able to regenerate thus the win would go to Kakuzu. Although I think that Kisame can avoid the black threads by ripping them apart via samehada and super strength. Kisame's sensory abilities and reflexes while fused in samehada should not be underrated either and I think he should be able to avoid those threads entirely if he fuses.