The ending made me think a bit. Basically, you've been through a grand total of 10 dungeons, you've defeated and helped to seal away the king of evil, and then you go back seven years and forget all about it, with no-one knowing what's happened. You've saved a country, yet you haven't because it now doesn't need saving and all the battles you fought you will never fight because they're in the future, seven years from now. (if you've never played OoT then you're probably hopelessly lost by now. Let's just say Occarina of Time).
It's a bit like Riven, in a way. In that one you beat the game, and save the people of the world by destroying their world. But weren't you trying to save it?
I do like it when the ending is more than a "You have defeated the Zorkans! Well done!" and then the credits. It shows just how much work has been put into the story behind the game.