Yeah, as much as people (Myself included) are not a fan of FE's over representation, it honestly like... Probably wasn't intentional.
Since we already had Mewtwo coming back, Roy was easily the most requested Melee Veteran to return (Well besides Icies, but 3DS). So he, along with Lucas for Brawl's returning character, were picked. Roy and Lucas are actually pretty popular picks among the casual crowds too, for some weird reason.
Then they wanted to have a character to advertise an upcoming Nintendo game, and at the time, the only real option that was far enough in development at the time was Fates. Therefore, Corrin.
So I don't think the over abundance of FE was at ALL intentional, in fact it was mostly coincidence, at least for Roy.