I've been reading through your chapters, JoshB, and first, I must say, your story's very good. It does seem almost like a playthrough in a way, but also clearly not at the same time. There are a few things I would caution you from overdoing, however.
Looking forward to more chapters!
- Punctuation and capitalization are both tricky in the heat of battle, when a lot happens all at once, but it does make it significantly easier to read. I would suggest such things as breaking a new paragraph when a quote comes in, making sure to use quotation marks on both sides of the phrase(s), and formatting attacks consistently. A pretty much agreed-upon format for a Pokémon attack is "Pikachu, use Quick Attack!" Note the comma after the Pokémon's name, and the capitalization on the first letter of each word in the attack. The exclamation mark is less necessary, but it never hurts. Just remember that practically every noun in the Pokémon world is capitalized and you'll be fine.
- The accented é is frequently overlooked, and while I do see it appearing in your story, it's not very consistent. It can be made by alt+e, followed by another e on most keyboards, I believe.
- You mentioned in a previous chapter that italics would signify the Pokédex, and I suggest you continue to do this. It makes it more obvious that the Pokédex is speaking.
- I like that you end every chapter with a cliffhanger, but ideally this is somewhat drawn out, by which I mean you've led up to it for a few paragraphs, rather than a problem occurring and reaching its climax in the space of a few sentences.
- There are a few instances in battle scenes where each paragraph begins with an attack command (i.e. Riolu, use Counter!). While this isn't a bad thing, It makes it easier to read if you include something like "...said Lavender" or "Roxanne exclaimed." Also, on the topic of battles, I understand that "Pokémon, dodge!" is very common in the anime, but frankly is a little overdone. Perhaps "Riolu, leap to the branch!" or something as a more detailed and less repetitive alternative.
Looking forward to more chapters!