I am not sure if it was said before, but I think Zelda II: The Adventure of Link should easily win this category. It is receives hate for being different and more difficult than other games in its series.
Metroid Other M deserves its hate not only from story but the linear level design. With that being said, Metroid Other M was still better than the bad EA, Ubisoft and Konami games.
Games I have Finished