My personal white whale in the "it would be good if it was good" category has got to be the Atelier Iris trilogy and follow-up Mana Khemia duology. In order, we've got a game that changed its core gameplay loop in the last leg of development and broke half of its subsystems in the process, an obvious rush job, a game that can't even decide what kind of game it wants to be, a game whose protagonist is so boring it's actually kind of inexplicable given how fascinating his whole deal is, and a game that actively punishes you for picking the female protagonist by giving her a party that doesn't meaningfully engage with half of its mechanics and a post-game that's functionally unplayable because it was never playtested with her in the lead. If you add up the good bits of all five games you'll have a collection of genuinely fantastic ideas on your hands, but every individual entry is irritatingly half-baked.
(To add insult to injury, the PC remasters just skip right past this entire segment of the franchise, so we've got updated versions of Atelier games from both before and after this era, but nothing within it, and none of the stuff that's interesting about them has ever been revisited in later entries in the series. Fun!)
