Surely you have played Phantasy Star IV. I think that was the epitome of Sega's RPG skills.

Another good one to watch for is the Saturn exclusive, Shining the Holy Ark - man that game was fun - though those pre-rendered CGI characters are not aging all that well.

If you like A Link to the Past then give Crusader of Centy a chance. It was released on Genesis by Atlus after Sega turned their backs on localizing it themselves in order to go with Beyond Oasis - another, similar, action RPG, also on Sega's Genesis.