Well, seeing as Kenshin's power is based on two things : first of all his insane speed and second his knowledge of martial arts in general if he were to face kakashi or any other decent Ninja I think he wouldn't last too long.
It is impossible to predict for him what the enemy will do nor does have any decent form of defense against it. You can't really block fireballs. Shuriken like attack would probably not be a problem. But summons, replacements, shadow clones, mind control techniques or even stuff like kaiten or gaara's sand etc... he can't really deal with those. After all Kenshin is human while most shinobi aren't
Also shinobi fight dirty in a way : any way to win counts so alot of their tactics are hide/backstab while Kenshin is more of a fair fight guy.
Sharingan and Byukagan aren't useless however, they can be used to see chakra and hands seals but they can also be used to see Kenshin's speed thus improving the users chance to defend.