Board Thread:Boruto Discussions/@comment-25319479-20160502145551/@comment-3965545-20160514023942

Jiraiya is using an imperfect Sage Mode, Mitsuki is using the perfect Sage Transformation which btw NOBODY else has perfected the Sage Transformation as Seelentau pointed out that even Kabuto said his Sage Transformation was imperfect. So the reason Mitsuki's traits and eyes are so different when using Sage Transformation is because he is the first person ever we know about who has perfected/mastered it. For all we know the eyes and the traits shown with it are common to all who perfect Sage Transformation, but we will never know because nobody else has perfected it, at least nobody else was shown with the perfected version.