1- Kisame has huge chakra but so does Kakuzu maybe not Kisame's lvl but still he has enough chakra to use high lvl elemental attack without showing siqn of exaustion.
2- Battle experience: Kakuzu severly outmatches Kisame since he has almost 80 year's of battle exp and is more smarter than Kisame.
3- Kisame can only use 2 elements kakuzu uses all 5 and can combine them at will and samehadha is shown to have weakness against high lvl fire attack(that can be boosted with wind), and if he uses all his mask then it is actually a 5 v.s 1 fight since they can move on there own and attack from any direction.
4- And main difference between them is that Kakuzu can survive being killed 4 times,since he has five heart so even if kisame manage's to land a lethal blow it will require him to do atleast 5 times, and Kakuzu's superior experience will come into play, when Kakuzu only need to kill Kisame once, though the guy is one tough motherfucker, so won't be easy
Also, Kisame may be able to gain advantage if he creates big waves of water element and his water shark missile could be dangerous range wise(since it absorbs chakra), which could be dangerous for Kakuzu regardless if he has 5 hearts or not, or at least if they're not seperated from his body
With 4 additional monsters walking around though, it gives him better opportunities to outmaneuver Kisame with his superior elemental affinities
Really hard to say, but i'd go with Kakuzu for now
