Hi Fisher,
What patch are you on? What were the levels of your team members and what scaling did you see that was broken?
I'm about to get to Route 119 in my own playthrough, I'll take a look and see if this is an issue.
NGL I had to look up mustelid! Unfortunately there is no FLY HM replacement, so that is still a requirement like in the base game. I couldn't really think of an alternative that wasn't like "Teleport Item". It could be possible to add a start menu option for "Fast Travel", but I'm not sure about the amount of work required for that. If I make any more major changes to this project, I'll definitely consider doing this.
I realized that I've been updating the Reddit thread but not this one! There is a spreadsheet
here that shows you all of the encounters in an area. All Pokemon can be obtained either by wild catches, in-game trades, or level up/breeding. Spreadsheet does not include legendaries - those can be found in the Pokepedia in your room ;)
Thanks for playing! Please let me know about the scaling bug and I might be able to determine what the issue is.