Ouch. Baten Kaitos, Terranigma and Rune Factory. You guys are hurting me.
And I'm taking a shot in the dark without doing much research here, but how about Lufia?
This one's a bit tricky since some more recent releases are retellings of the story of previous entries in the franchise, so I'm unsure as to how to treat e.g. the DS release since it's a re-release of the original second SNES game, despite the change in game mechanics (turn based to action RPG, 2D to 3D). Also, the last game that wasn't a retelling,
Lufia: The Ruins of Lore on GBA, is designated a Gaiden (sidestory) entry and I'm unsure how that counts. Still, either the GBA or the DS entry had solid reviews.
Before that we had the GBC The Legend Returns which seems to have been the only somewhat bad entry. So that'd be a strike against my submission if we were to discard these two last entries.