She's got a sword, R Blade, and she's fast with it. And at least one gun that can bend space. And triple vulcan cannon. Besides, are her hands supposed to be restricted? Is this really Kos-Mos??? (playing Episode III right now)
Hey, she had multiple alternate forms. As a matter of fact, I believe that the archetype had yellow eyes. Besides, who's to say what color her eyes may turn once she awakens on Lost Jerusalem?
The series still has three games yet to be produced. Although Shion's story arc is complete, that doesn't mean she won't appear in the next three, with KOS-MOS by her side.... with yellow eyes.