Currently, in PRO, a tree axe can be used to cut those pesky trees that get in the way. There also exist, a pick axe which is used for smashing those pesky rocks that get in the way.
My well thought-out suggestion is to implement a shovel, a headbutting helmet, a lantern, and rock-climbing boots.
Shovel:
The shovel would make it so you don't need a Pokemon with happiness to use dig on the dig spots throughout the game.
Headbutting helmet:
A headbutting helmet would make it so you don't need a Pokemon with happiness to headbutt trees throughout the game.
Lantern:
A lantern would make it so you don't need a Pokemon with flash to lighten up the dark caves throughout the game.
Rock-climbing boots:
Rock-climbing boots would make it so you don't need a Pokemon with rock climb to scale yourself up the rocks throughout the game.