Oh, I think you might want to fix these:
Sora, driving the Gummi Ship with diligently, was quite aggravated. This is so now what I wanted to do on my sixteenth birthday.
Dilegence, not diligently in this context. And I aslo beleive that the 'now' was meant to be not. LoL, Sora's sixteen now.
Lastly, Sora’s weapon, the Keyblade, a mysterious yet ominous weapon in the shape of an oversized key in the shape of a sword – or a sword in the shape of a key, if that makes any more sense – a weapon that, depending on its owner could bring salvation or destruction.
That's quite the sentance ^^' Perhaps you might like to cut it down some.
I'll help you some more when I get back, but I've gotta go.
EDIT: Guess who's back? So, I have just finished this prologue, and here's some of my thoughts:
1- Pokémona Encyclopediae Zexi -- I was a bit confused by its sudden appearance. Did it just appear out of thin air? It might be a good idea to describe a little bit more of that part. I wish I could remember which one Zexion is, but this idea for the book is neat. I guess it will act as a Pokedex for Sora?
2- Giratina is a big Pokemon, right? You might want to go into detail about it, 'cuz it seemed to me while I was reading this it seemed small. Maybe that's just me, though.
3- Maybe go into a bit more detail about the distortion world, yes? It kinda seemed vague.
4- Why would Sora be upset about traveling on his B-day? I would think that he'd be excited, since he likes exploring and stuff.
I wonder why the heartless are in the Distortion World, and what Zexion did while he was in the Pokemon Universe . . . I also wonder what Marluxa (I think that's spelled right) wants with Ash . . . It will be interesting to see how you incorporate Cyrus into all of this. I'm excited! ^^