reasons why kakashi can beat kisame is ability to adapt to the situation.combat experience(kisame has experience but more on assassination, bijuu capture, and recon etc.) while kisame does have far greater amount of chakra he lacks diversity in his jutsus and kakashi's sharingan will exploit that. now don't get me wrong i don't think kakashi will take him out like a chump after all Guy-sensei did have to open 7/8 gates to smash him. as far as samehada goes, kisame gets more use out of samehada in stealthier situations rather than combat. other wise samehada is just a living sword that shaves instead of cut while absorbing chakra. kakashi's speed means that he wont be an easy target and his MS is basically a 1-hit KO. so to conclude what kisame has in chakra kakkashi has in skill.