Your title has been edited. Also, take care not to double-post like that again.
You should work on your paragraphing. All of your paragraphs are just a sentence long. Since I didn't see this story when you originally posted it, I'm not sure if you made the paragraphs this way after or before you received some reviews.
Let's take the opening of this chapter, for example. Instead of each line being broken up like it is, let's combine things into better paragraphs.
A young pokemon trainer named Touko was strolling up Route 1. Her flowing, black and beautiful hair swayed in the wind. She was wearing a white cap with a crimson coloured pokeball on it. She also wore a white t-shirt with a black jacket. She had just left her home of Numeva Town.
The Route was long and grassy, with trees dotted here and there. There were people too, probably other Pokemon trainers. So many thoughts were rushing around in her head: Would she have a good adventure? How many pokemon would she catch?
It looks much better now, doesn't it?
I just noticed that you have a lot of sentences that start off with "she" in that first paragraph right there. Since you want to include Touko's description in this fic, you have two options to write this better. The first thing you can do is combine sentences:
Her flowing, black and beautiful hair swayed in the wind, mostly tucked under a white cap with a crimson coloured pokeball on it.
You can also reword the sentences so that they don't start with she.
Or you can spice up your descriptions by making them more alive than a list. Instead of saying that Touko wore a white cap, say something like "She dusted off her white cap." Something like that. That way, the description becomes more memorable and stays in the reader's mind.
Like bobandbill said, you should break away from writing just the basics of what happened in the games. Add more to it, like Touko's emotions. Don't just say that she's happy to be a new trainer. Say things like "Her heart raced in her chest" or however Touko's emotions make her respond.
Remember to keep characters' characterizations in mind. Like would N really compliment Touko at all, especially since he doesn't like humans? N's a difficult character to write well in romance fics, so take care not to rush anything with him. Keep his back story in mind.
Another thing you should keep consistent is the capitalization methods for Pokemon and the species names. You start off not capitalizing "Pokemon" but then in the same chapter you start capitalizing the word. Make sure that you consistently capitalize it and related words or not capitalize it and related words, depending on which way you choose.
I also saw that you capitalized "professor" in the scene with Juniper. Unless you're using the word as part of her name, it shouldn't be capitalized. You'll probably want to look around for a beta reader to help you with grammar.
Hope this helps.