Well, no one else seems to want to judge so I'll just begin then.
MS Sasuke Uchiha is no doubt a very powerful shinobi. A testament to that is he defeated Danzo after a tough fight against 4 kage. However, he would lose to the Akatsuki's Kisame Hoshigaki mainly due to the fact that Kisame is a very bad matchup for him, and can counter Sasuke's entire arsenal with relative ease. I'll start with 3T Sasuke's arsenal.
Genjutsu: Sharingan
A generic Uchiha genjutsu, which is cast upon the user making eye contact with his opponent. Indeed it can prove useful, but using it is useless against Kisame. He has 3 counters to this genjutsu:
1)
He doesn't look into Sasuke's eyes. Kisame, being Itachi's partner, is well aware of the Sharingan's visual prowess and knows not to make direct eye contact with an opponent who has the sharingan.
2)
Merging with Samehada and closing his eyes. As we know from Kisame's battle with Bee, Kisame does not need his vision in order to do battle with his opponent, since he can sense chakra. A testament to this is that he knew Bee's exact location despite not being able to see anything through the ink.
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3)
In the unlikely event he gets caught in genjutsu, yet Samehada breaks him out. Samehada has been proven to be a living organism capable of absorbing, devouring, and sharing, chakra. Logically, Samehada can also disturb his owner's chakra, which would break Kisame out of genjutsu.
Chidori and chidori variants
Chidori and chidori variants such as Chidori Nagashi, chidori sharp spear, and chidori senbon are all classified as lightning-style ninjutsu. Unfortunately for Sasuke, they are all useless against Kisame, as Samehada has proven more than capable of absorbing Raiton:
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All Kisame has to do at this point is merge with Samehada, and Chidori will be absorbed before it can injure Kisame.
Another point to make about Chidori: my opponent seems to believe that lightning is elementally superior to water: that is not the case. While it's true that water conducts electricity, the lightning will not electrocute Kisame because when he is merged with Samehada, he can absorb chakra through his skin. The lightning in the water gets absorbed, with no harm to Kisame.
Katon: Goukakyuu no jutsu
It is almost not worth mentioning this point. As we all know, Suiton > Katon. Kisame is easily the best Suiton user in the series, and he can easily counter Sasuke's katon with
Suiton: Suikōdan no Jutsu or
Suiton: Dai Bakusui Shōha
Kirin
Kirin is not happening in this fight. It requires katons and prep time, which Kisame is not going to let fly. The only time Kirin has ever been used, it required 2
Katon: Goukakyuu no jutsus from Sasuke, two from Itachi, four giant fire dragons from Sasuke, and half a forest lit on Amaterasu. As I said earlier, Kisame uses his Suiton to easily extinguish the flames. Unless this battle takes place during a thunderstorm, Kirin is simply not an option for Sasuke.
Now we move on to Sasuke's Mangekyou arsenal.
Amaterasu/Enton
Amaterasu involves the ignition of black flames on whatever target the viewer eyes. Enton involves the manipulation of the black flames. Neither of these jutsu pose a problem to Kisame. When he is merged with Samehada, he has been shown to absorb ninjutsu, including fire-style chakra:
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Now, my opponent used this exact same scan to show that Samehada couldn't absorb katon, when in fact it proves the exact opposite. Samehada successfully absorbed the katon completely and fully; the fact that it 'thunked' Bee on the head afterwards shows mild irritation, not inability. In fact, my guess is that Kishi included that simply for comic relief. My opponent also says that absorbing a katon is different from absorbing Amaterasu, which is superior. The fact remains that Amaterasu is still, at its core, a chakra-based ninjutsu, and therefore can be absorbed by Samehada. The only time Samehada will not be able to absorb ninjutsu is when it is simply overwhelmed by the amount of chakra, as seen when it could not fully absorb Bee's V2 state. Amaterasu does not contain excessive levels of chakra, or else Itachi (who had low stamina/chakra levels when he was alive) could not have used it.
Susano'o
The susano'o is a massive spirit-warrior which is a physical manifestation of chakra that provides all-around defense for the user. Even this, Kisame will be able to deal with fairly easily. Kisame spits out his
Suiton: Dai Bakusui Shōha, a gigantic dome of water that totally dwarfs MS Sasuke's Susano'o. Once Sasuke's Susano'o is surrounded by water on all sides, Kisame's victory is assured. Kisame is not getting injured by the Susano'o so long as he stays out of its range. A good 50 meters is probably enough for Kisame to stay out of harm's way. Sasuke cannot swim up after Kisame, because his Susano'o is legless, and if it comes off the ground, it will instantly flood with water, drowning him. In fact, Sasuke's susano'o is completely immobilized at this point due to the massive water pressure weighing down upon him (this is assuming the water pressure doesn't outright crush his Susano'o). Even if some restricted movement is allowed, Kisame's speed underwater > Sasuke's speed, so Sasuke is not going to get close enough to Kisame to use Susano'o against him.
Susano'o arrows
Unlike Amaterasu, Susano'o arrows are long-distance attacks that cannot be absorbed and probably Kisame's biggest threat. However, at this point Kisame is in his water dome, about 50 meters away from Sasuke. Kisame is extremely fast underwater and can dodge the arrow from this distance. Something else I'd like to point out: Kabuto, who is not particularly fast at all, managed to easily dodge a Susano'o arrow from a shorter distance than 50 meters. Why? Because he has sensory skills and can detect chakra, even without sight. Kisame is the same. When merged with Samehada, he can sense chakra through his skin, as I stated above. Kisame can know exactly where the arrow is going to hit the moment Sasuke lets the arrow fly, and be sure to avoid that spot. So even if Sasuke goes straight to Susano'o and spams arrows at the beginning of the fight, before Kisame unleashes his water dome (which is not in character for Sasuke at all), Kisame can avoid the arrows despite not being underwater, so long as he is merged with Samehada.
Now we move on to Kisame's counterattack. Kisame has two main options for defeating Sasuke. I will list them as option A and option B.
Option A
Kisame floods the battlefield with his water dome, and Sasuke is a sitting duck in his Susano'o, surrounded by water on all sides. Kisame uses
Suiton: Daikōdan no Jutsu (otherwise known as Great Shark Bullet) to finish Sasuke. As I said earlier, the Susano'o is a physical manifestation of chakra. The characteristics of Great Shark Bullet is that this jutsu absorbs chakra from an opponent's ninjutsu. Kisame stated that the stronger the opponent's jutsu, the stronger the shark becomes. Therefore, Great Shark Bullet attacks the Susano'o head on, and absorbs his entire Susano'o and wrecks Sasuke. Once his Susano'o is gone, Sasuke drowns. GG
Option B
Kisame plays the waiting game. In case it isn't obvious, Kisame is a chakra monster, a testament to that being he was known as the Tailless Tailed Beast, and he spit out lakes against Team Gai when he only had 30% chakra. All Kisame needs to do is maintain his water dome, and Sasuke either goes blind from overusing Susano'o, or retracts Susano'o and drowns. Without the eternal Mangekyou Sharingan, Sasuke cannot maintain MS techniques for very long, and Kisame easily outlasts him. Kisame wins.
Conclusion: Kisame wins this mid-high difficulty.
