FFXIII is really a great example of a game getting both better and worse in the latter half of the game. After chapter 9, the story went downhill fast, and dashed all my hopes for the game. But with chapter 11, the gameplay became much more interesting.
Another one for me is FF7. I think the first disc overall is really good, but shoddy writing makes the second and third discs very disappointing. They should have just ended it at Aeris's death and the ending would just be everyone dying.