Before it wasn't like that, but lately a number of characters have an eye color - hair color match it. It looks better, I prefer the new looks (HGSS characters) and I couldn't imagine most characters with different eye colors, but still..
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The point is that it reduces the number of colors which need to be used in sprites. A trainer's sprite typically has a limited color variety, and by having the eye colors match, Game Freak can include more colors in the outfits.
As for why they changed at all, it's due to the fact that Ken Sugimori's art style now utilizes eye color, while it never did so in Generation II.
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