My choice would be Breath of Fire: Dragon Quarter. All of the people I knew loathed it for being a big departure from its traditional RPG predecessors. The biggest "sins" were with the "D-Gauge" system, a limited resource that slowly trickles away and could never be recovered; if it reaches its limit, it's an instant game over. Unlike in the previous games, dragon transformations greatly consumed from this "D-Gauge", and as such, made it very painful to use in the long term. That the hero was only limited to one dragon form didn't help matters for them either. Other gripes included very small character count (only 3 playable, 1 other temporarily), a drastic setting change (bleak, underground themed magi-steampunk instead of a more traditional fantasy setting), limited exploration (linear, winding paths through a looong dungeon instead of an open world), and ramped up difficulty (very few permanent save points, and no rest or recovery spots along with few ways to heal without items).
Honestly, I couldn't understand why they hated these changes as much as they did. As I saw it, the D-Gauge and limited health recovery methods added a strategic challenge through attrition, giving an appreciable sense of urgency to the story itself. This, along with a more mobile combat (more TTRPG than traditional RPG) and an actual fondness for dismal, hopeless settings allowed me to look well past those other percieved "flaws" above.