Well I still hope the FE13 Roy is the main Roy. I think FE6 Roy and manga Roy can kinda be merged together, with a different colour Roy getting the lighter armor/cape that the manga one has. I think the Melee Roy can be further differentiated by accenting the comparative darkness of his hair and cape and possibly increasing the intricacies of his chest plate and head band. Just my opinion though.
And IMO:
FE13 Roy > Manga Roy > FE6 Roy > Melee Roy
(just based on aesthetics)
And IMO:
FE13 Roy > Manga Roy > FE6 Roy > Melee Roy
(just based on aesthetics)