MS was not equal to Rinnegan but he still in a way 70% defeated Edo Nagato. It is the user not the power that matters. Plus why wld u consider a sick person for a fair match?The EMS is not equal to the MS. And Itachi is sick.
Also how an Sasuke's EMS wld counter Tosuka blade and Yata mirror?
Also as far as other factors goes Itachi has much more experience and was hell lot of more talented from the beginning.