Kakuzu vs Kisame, interesting matchup.
Both extremely durable, but Kisame's durability stems directly from Samehada....Let's not forget something here as well. Even with Kisame's lake advantage, Fuuton/Katon is plenty to counter it. As for the Water Dome thing, he needs to have the TIME to fuse with Samehada, but, what is more, we know Kisame absorbs chakra through the water when fused with Samehada, but we DO NOT know if he can absorb elemental attacks when fused. My bet is that he sacrifices the sword itself for durability, speed, strength, and chakra absorption via water.
With this in mind, we can deduce a few things.
1. Kakuzu in no way has bad stamina. He used jutsus that would deplete Kakashi's chakra pool in one or two uses.
2. Kakuzu definitely has the elemental advantage, whether it's Raiton or Fuuton+Katon combinations.
3. Kakuzu has the same range as Kisame does, and as great of a mobility stat in Jiongu as Kisame does in the water during Samehada fusion.
With this in mind, I could easily see Kisame electing not to even fuse with Samehada, but rather fighting him in the base and relying on Suiton: Daikōdan no Jutsu and other water based elemental attacks, like he unleashed on Maito Gai.
The real test here is whether or not Kisame can keep up with Kakuzu's roaming masks, while accounting for Kakuzu's main body. All it takes is one misstep by Kisame and he's impaled by the Jiongu's threads, and at the same time getting Samehada pried from his hands.
Conceivably I can see Kisame taking this just as easily as Kakuzu, but I do believe Kakuzu would win more often than not.