Cute. I think it’s too bad we don’t see more of Marley on this site. But this was adorable and well-written. A mistake I noticed was when you started one sentence with a number, but that’s about it. Keep writing, fellow author. :)

Hi! I’m doing a round of reviews around the site, hoping to help give people constructive criticism instead of just vague appreciation or flames. If you do choose to take my advice I will be glad, but you don't have to feel like I'm making demands of you. I usually try to point out things that could help with future stories, so they can be useful even if you don’t want to edit the current story. Feel free to disagree with my interpretations and don’t be afraid to let me know why. I will be pointing out grammatical errors as well; please understand that I am not trying to be judgmental, but that I honestly believe corrections can improve the story.

I appreciate that you’re not capitalizing pokemon. However, you shouldn’t capitalize species names either, for the same reasons.

[the blue-haired youth]

Drawing attention to odd anime visual riffs is awkward in prose. It’s probably a better idea to keep to real hair colors.

[the professor Oak]

When titles are appended to names, they are capitalized. So this should be “Professor Oak”.

[Kanto and Johto's foremost pokémon authority]

Aw, does Elm not get any respect? :p

["I... I don't like to talk..." the newcomer, an elegant looking girl with short black-hair, dressed in a frilly black and white dress, spoke.]

“Spoke” is, ironically, not a speech verb, so the narration here needs to be a separate sentence.

[completely unaffiliated with Oak, mind you]

The general you sounds awkward in third-person, so I’d recommend rephrasing this.

[Doesn't that happen to almost everyone who goes on an adventure?]

The rest of the story is in past tense, so this should be as well. This applies to all narration, even thoughts. You can write thoughts in present tense, but they need to be italicized or have some other marker to distinguish them from narration.

[Lucas just couldn't help it, he went speechless.]

This is a comma splice. You need to split this sentence in two or use a different transition.

[In an instant, the boulder flashed in a blinding light; obscuring the entire route.]

This is improper semicolon usage. As a general rule of thumb, you should be able to replace semicolons with periods and still have the resulting sentences make sense; for instance, what I’m doing here. A comma would be fine here.

[What once was an uninteresting, dirtied plateau, was now a wondrous garden.]

The last comma shouldn’t be there. If you have trouble with sentence structure, I’d recommend getting a beta reader to help you.

[5 seconds later]

In prose, numbers less than 13 or so are written out with letters.

["So, what happens now?" He suddenly asked]

Dialogue formatting rules remain constant regardless of punctuation, so this should be ["So, what happens now?" he suddenly asked].

This is decent, but the opening bit feels awkward, as the wooden game dialogue is at odds with the quippier dialogue you give Lucas. It’s also weird the way he talks so little there when he’s so chatty at the end. Sometimes it’s best to adjust game scenes a little to more naturally inject the PC into the conversation.