Most of the obvious picks have been chosen, so here's a new one:
I am bitter about the second half of Legend of Zelda : The Wind Waker being cancelled/scrapped. We know there were more dungeons planned. We know they were worked into Twilight Princess somehow.
Forever, in the ages of history, The Wind Waker, for all it's beautiful and timeless animation, music, and uniquely awesome setting -- we have an unfinished second half of the game hampered by one of the most egregious padded fetch quests in gaming history. Even the remaster still included the fetch quest. It really is a real shame. I remember playing it the first time thinking it was unequivocally the best game I had ever played. It was incredible. Then it falls off a cliff and the second half is a barren wasteland, giving you no new towns, no new islands of significance, and making you sail over the entire map realizing how empty and boring it is. The magic was lost. It was like a delicious and beautiful pie being cold and uncooked in the middle. It was simply unfinished.
It saddens me to this day that what could have been an ageless classic is now an unfinished product, all because the GameCube was struggling and they needed it out as fast as they could.
