If Kisame manages to get a large mass of water out, then yea he wins. However, if they both are fighting on top of a mountain, i think Kakashi would stand a good chance. Samehada comes into play, then everything is in Kisame's favor.
Kakashi is bieng underestimated, If they are fighting on the ground, kakashi can use the earth style technique where he drags his opponent into the ground, and chidori/kamui kisames head. However this would only work if he used it before kisame makes that giant buble with water. However even then kakashi has options such as substitution and clones.