Board Thread:Naruto Discussions/@comment-24347194-20150412182932/@comment-4271790-20150412185356

Also, a common misconception is that the EMS is stronger than the MS in the sense that it unlocks certain abilities that the MS can't do. That is not true. The MS is just as capable as the EMS, proven when Kakashi and Indra used the Complete Body Susanoo with just an MS, and stated in the databook that the CB Susanoo is awakened with the "power of the Mangekyo," not the EMS.

The EMS is "stronger" than the MS in the sense that it is more durable than the MS to withstand the usage of many MS techniques without becoming blind. When Kakashi said that the Six Paths Power made the eyes "stronger," it meant durable enough to withstand the usage of the CB - Susanoo and other MS techniques without becoming blind.

But yeah, all the EMS does is allow the user to utilize the power of the Mangekyo Sharingan an endless amount of times without the side effect of becoming blind or experiencing "pain in every cell of the body." Still, the MS is just as capable as the EMS, it just has a bad side effect before getting there.