This is just based on my experience, but Japanese animation tends to show certain physical cues to identify character traits. A few examples are hair (only applies in some cases, but bad characters' hair tends to cover their eyes and face), body build (good characters tend to look less intimidating than villains), and eye color. The last one, eye color, is generally the most subtle of the techniques they use, but it's also fairly important because of how much emphasis japanese animators tend to put on the eyes. Blue is in fact a color very often used to indicate good guys (though in some cases it can be used for important bad guys as well), and you'll notice that only Sora, Kairi, Namine, and BHK sport this color in the game. Riku's eyes are in fact, if I remember correctly, a very vibrant shade of green, and he had a role very different than that of Sora and the others (though not necessarily that of evil, at least before Ansem possessed him). Ansem himself I don't remember, but I thought it might be an odd goldish color.
This is, I must admit, a rather long and complicated post to answer that one question, but I think the reasoning is at least fairly sound.
