Reading your initial post, you missed
Chrono Trigger, had a sequel in Chrono Cross and that was it.
Lunar Silver Star Story, followed by Lunar Eternal Blue, nothing since (perhaps you can count that DS offshoot or remake??) Its anime cut scenes and voice acting were great (I know the cut scenes were enhanced later on).
Dragon Force, had a sequel in Japan only, was an excellent albeit repetitive at times strategy RPG, perhaps when Working Designs failed (company who localized the first one) any hope of seeing more went away?
and ofcourse we can say Baldurs Gate is missed, though I believe it was an expired license that ended that franchise after the second one and forced the third one to be an expansion to the second game.