Good to know Pia liked it! I wold like to say that my Essentials GS is like a Pia's Gold Engine "reborn", he he he! These days I've been a little occupied with my job and studies, but I'm still developing Crimson & Navy, I still have a story to tell!
Oh, and about the Gym Leaders teams, they actually change, or better to say, after beating two of them, the other 2 gyms add other two new trainers while the other ones get stronger, and the leaders add another pokémon to their teams as their first one to battle, and the other two evolve or get more levels.
PD: There's a button called 'edit' in your VMs, you can use it to fix your messages, he he he!
The top left corner boost animations bug is from Essentials itself, so I don't know how to fix that, maybe Maruno would know, he he he!
Pokémon Crimson & Navy was made with the Version 13 of Essentials, so I don't know if Versions 14 or 15 have fixed that boost animation bug, I'm going to download V15, so I would study it and then to think about moving the game to V15 or not.
For now it's not possible to revive the fossils until the final version, I'm still thinking about where to put the pokémon fossil expert, he he he! For now, before I continue with the game, I have to fix the bugs you discovered, and maybe another ones we'd find out soon.
Seriously, thank you so much for your feedback! This project is getting followers slowly, but it's just a matter of time until it gets more. Thank you again!
You're almost done! Now that you got the Poké Flute, you can battle and catch the Snorlax near Conduct City, and if you want, you can take the Sudowoodo sidequest too, but I think you can figure it out for yourself.
Your friend is rising her/his pokémon just like every other trainer in the game, so in terms of story, it's just a thing of logic that they still aren't equally balanced in levels yet, you can assume that Wurple had been catched or put in your friend's team recently, and so, it's still in training.
And about her/his Charmander, well.... Have you heard about the "B button" thing? or in the the case of Pokémon Essentials games, the X key.