NES: Hydlide is a pretty solid answer so I'll go with that.
SNES: Man I really don't think Mystic Quest is good at all. It's bland and dull.
PS1: Persona 1, particularly the North American version, is awful but I'd have to go with Beyond the Beyond simply because it's cliche to the point of parody. Shadow Madness and King's Field are good second picks.
PS2: Star Ocean 3 is full of awful JRPG tropes but the combat is fun. For me it's gotta be Shining Tears. Ugly and boring.
PS3: Yeah FFXIII is pretty bad and a failure of game design but it works competently and has passion behind it. Enchanted Arms is pretty not-good though, full of cringey anime tropes that unlike series like Hyperdimension Neptunia or the Atelier series, isn't absurd enough to be endearing. Though for my money the worst RPG of this era is Star Ocean 4. A game of lowest common denominator weebs and an example as to why JRPG's kinda fell from grace for a while.

I really liked Dark Cloud/Dark Chronicle, it's closer to a proper roguelike than most of the games being slapped with that term nowadays.