I just finished Mark of the Ninja and while it's a really good game it just kept introducing new game mechanics and dragging on. On multiple occasions I thought the end would and should be near, but it wasn't. Luckily the ending was strong when it did show up.

Ni No Kuni had a similar situation. I feel like halfway to 2/3rds of the game is filler and during this time I felt like it should get on with rounding up things. Again the ending was strong, but should have come around sooner imo.