Super Mario RPG
This was Square taking on the Mario franchise, and it took it to very weird places. Being Square in the heart of their JRPG golden years, they definitely delivered on a great and fun RPG... but something was a bit off. The Mario characters they used were done great, but Mario RPG introduced a number of characters that have never been seen again. Not only this, but the bad guys did not suit the rest of the Mario franchise built up before Mario RPG in look or tone. This all cumulated into a Mario game that didn't feel like it was in the Mushroom Kingdom (much like Mario 2 on the NES, but that's because it was all a dream). Despite the odd tone, the game was fun... really fun. A simple and cute and funny JRPG that is still loved by many.