I love pixelmons boss system it so good :D
It doesn't seem to fit here though its likely to just majorly confuse new players to the game and make them ask a bazillion questions
maybe instead a boss pokemon could be added to each area of the game say a lvl 60 Arcanine at a 0.1% spawn rate on mt ember and it always holds the tm overheat i'm sure there's enough areas to add one for every tm and it would add a lil extra challenge to going through the game.