Gundam 00 Headcanon 10/?

 The super-soldier-making process produces people with gold eyes.  Not consistently, not everyone–Allelujah’s fellow escapees seemed to have dark eyes, though only one of them was ever onscreen for very long, and he was only ever in greyscale that I could find.  But particularly with the first hundred subjects, the scientists used a lot of different approaches, varying them from subject to subject and some of them in certain combinations did lead to changes in eye color. 

 

Frankly, there’s not a lot of real science behind the idea of changing an already-born human’s eye color (and I’ve already said that I think Allelujah was born before he was taken to the Institute)…but a lot of not-scientifically-possible things happen in this show.  And it makes more sense than the show’s two super-soldiers both naturally having gold eyes, with the one who was considered imperfect only having one.  Especially when you consider that Innovators and Innovades’ eyes turn a sort of kaleidoscopic gold color when they use their abilities.