>>34114598(I hope)
Instead of having HMs and PokeRides, you can trade berries with wild Pokemon so they'll help you smash a rock, move a boulder, cut down a shrub, surf across water, etc...
You press A on an obstacle and you'll be asked if you want to lure a wild Pokemon to assist you. A wild Pokemon will appear, and you'll offer a trade with it (e.g. I'll give you this Oran Berry if you chew down this shrub for me).
Each island will need to have markets/people that sell berries before obstacles. Each kind of obstacle requires a different kind of berry.