Kakuzu has lived over a hundred years which makes him more experienced then kisame(regardless of that fight with naruto :|)
How does he beat kisame? By turning it into a 5 vs 1
He has the advantage with
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which is two streams in one making it harder to dodge and was only countered by kakashi's lightning cutter.
Kakuzu is can also be a long ranged fighter since kakuzu knows about samade he would avoid it and beat kisame in a long range fight with his 4 hearts swarming kisame while his arm can burry under ground for sneak attack. If push comes to shove and kismae traps kakuzu in his water dome, with his lightning element mask he could shock the water stunning or killing both of them. Kakuzu can then escape or be revived with another heart