I disagree on the vanilla, although I absolutely agree on the stereotypes. There are plenty that it falls in to.
But where I disagree is on the story. Really, it's a terrific story and as said above is awesome because of the sum of it's parts. Your not just time traveling, but your creating history as you do it. It starts out with the lone sword wielding boy waking up, which is fine, but from there, he's not kicked out of his town then forced to redeem himself. No no, he's basically doing Luca a favor because he knows that her career is over and he's lost a friend if he doesn't. Not to mention, just doing it because it's the right thing to do. None of that "Oh no, she's lost, what should I do?!" crap. No, just picked up the amulet and went after her without a word of whining (I'm looking at you FFX)
Also, none of that, "I'm the village elder, A mist has taken over the land, you as the youngest least experienced child, must go defeat Cthulu, dark emporer with a crummy training sword. Good luck! Oh, and no discounts at the shops." It's more like, "So, we've been time machine. Wanna see how the world is destroyed? Okay, lets go. Ohhhh, big monster, I thought it'd be global warming. Want to stop it? ....k"
End of Time
6 distinct time period, with 6 maps
Frog and others are extremely memorable
A superman-esque time machine
Your friends save you and keep freaking time from destroying itself by replacing you with a freaking clone!
Robo, you build a character, which wasn't normal back in the day