Pain easily defeats Shisui with no difficulty. He has the Rinnegan which allows him to use all of his abilities and even capable of destroying the village in a single push.

Some of you will say Shisui can cast kotosmatsukami but this will not work on rinnegan. Then again some of you will say Itachi in his edo tensei was able to defeat pain with his mangekyo . This was because Itachi discoverer his blind spot as nagato was handling all the abilities of pain single handedly. That will hardly work against six paths pain. The only way to beat pain is rinnesharingan (sasuke), sage mode Naruto or six paths Naruto. No one else can beat pain. PartyCity Feedback

And only white mask Obito can beat pain since he has rinnesharingan and Senju cells. To beat pain one should either have a huge chakra reserve along with sage mode or rinnegan