Uh, wow. Could you maybe hop in the discord so we can discuss this somewhere easier than the game's comments section? That's a lot of things to fix!
-- The bugfixing's done and it's been uploaded, though the level cap thing is intentional. 10 is the limit for MERCANOID. Level Cap sets an increasing level cap that scales with Main Quest progress, it's for people who don't like to over level for an area's intended difficulty - akin to Pokémon Nuzlockers not going over the level of the next Gym Leader, as an example.
Everything else is potentially useful, but I would need more discussion on it before implementing any of it. My code is jank, but it's jank I understand, and I've been burned by relying too heavily on proper big-girl code I didn't understand in the past.