To me, this Shisui is designed to counter super armor instead.
His dps seems to better than Kakuzu too.
Regardless, it comes down to the different in power.
yup he is designed to counter existing meta in cn like kushina, kakuzu, killer bee and even minato since shisui has undogable mystery(for minato) , super armor suppression(for kakuzu) and locks opponent mystery for 2 round (for all 4 of them)