Despite my hate of XIII, I actually don't mind Xenogears 2nd disc but that's because they waited until I was completely invested in the story to pull what they did.

Legend of Mana has a rather sub-par ending, the game really doesn't try too hard to tell an overarching story with the Mana Tree, so when it finally shows up, and you face the final boss, its not as well done as the Dragoon or Jumi Tribe stories. It's a shame cause overall, it was a great game.

DQVIII petered out by the end as well, I literally was thrown off that I had reached the end and when I beat the Final boss, I was expecting another form, and instead went straight to the ending.

I would agree with FFXII, but only in concern with everything that takes place after the Pharos dungeon. It really reeked of a rush job but, I still give Vayne props for being a more challenging boss than most of the modern era FFs.