You had too many things that differed from canon.
For example, Spectrum Town and Sienna City. They don't seem necessary to the story in any way, and you seemed to add them in there just to have something to set yourself apart from other fics. Setting yourself apart this kind of way isn't necessarily a good thing.
Also, you seem to like the spelling of "Buoysel". But that's wrong - you really should change it to "Buizel".
You might also want to reconsider "Professor Maple" - there are too many name-of-tree professors out there already, and Maple is one of the common ones. Using this makes your fic seem naive and clichéd.
Fourthly, Rachel and Ken seem to be finding Pokémon in the strangest of places - there's never been a Skarmory in the Kanto region or a Pikachu on Route 1, and especially a Lapras in Viridian Forest. If you keep doing things like this, it makes your characters seem more like Mary Sues, because they're getting into the strangest situations for no reason at all but the author's whim.
Last of all, you renamed all the route numbers. Why? What was so wrong with the original route numbers that you just had to change them?
In conclusion, you should consider making your story closer to canon. The way it is right now is more like original fiction than a real Pokémon fic.