Fixed a heap of errors, and explained more about why Juniper is here, other than the fact that I find Elm annoying and like her a lot more.
Personally, I'd say to get rid of the prologue. It's really not needed, since it doesn't add anything to the story. Pretty much as soon as Indigo gets to the lab, we find out that Team Rocket is there to steal Pokemon. Why they're doing that since they've disbanded, we don't know, but I'd guess that's one reason why Indigo goes on her journey. Still, there's some grammar errors I can point out.
Thanks for all the advice!
EDIT: After some pondering, I think the other reason this needs so much work is that it's just made the trasnition from daydream to Fanfic, and the stuff I can see in my head isn't just going to magicly appear for everyone else. Need to work on that one. :s Not sure how yet.