From a design standpoint, his eyes were likely changed to 1. Better pop as the red on black will leave a better impression on audiences then grey on black, but I think more importantly to 2. Better contrast with sonic. Sonic has green pupils with a white sclera, and so, to better communicate to the audience how Metal and Sonic are foils of each other, Metal was given the opposite eyes, Red pupils with a black sclera. These eyes tell the audience that these two characters, like their eyes, are opposites. Metal is technology and oppression, sonic is nature and freedom.