Well, I was a bit disappointed to see Kid Icarus:Uprising ending after 9 levels.
Katamari Damacy was a bit on the short side, although admittedly this last level to make the moon is just outright awesomeness and the end credits are fun too.
With Zelda:BOTW I kept avoiding going to Ganon, because I didn't wanted the game to end.
Monkey Island 2, because it was a great game, but I hated this ending.







