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.
I've been playing Crusader of Centy for an hour now and absolutely love it.. at first I thought okay this is totally a Link to the Past clone but after playing it some its definitely more than that.. I'll try Beyond Oasis after this one... haven't had this much fun with this type of game since Hyper Light Drifter.
I will have to check out Hyper Light Drifter. Never heard of that one.