User blog comment:MMB The Coolest/Regarding Roy (Fire Emblem) and Roy (Koopaling)/@comment-24503190-20140921145604

The reason they didn't bring back Roy is because he only appeared in one game on the Gameboy Advance and is in no future Fire Emblem titles. In fact, they only had Roy in Melee to get Japanese gamers hyped for Binding Blade, which hadn't come out yet, so there really would be no reason to bring him back. I'm sure they had decided to not bring back Roy long before they decided to make the Koopalings alternate costumes.