User blog comment:Kaloneous/Mass Effect 3 Ending DLC Denied and PAX/@comment-4937645-20120510220059/@comment-1341687-20120512061155

The eyes change because they are both endings in which Shepard embraces the Reapers and at that point it's just the melding that is coming through. It's a visual cue. As well as Shepard was clearly revived with Reaper tech (personal opinion) and that's what makes those two options even possible.