Well here's my detailed thought about how we could balance the system.
Stones for certain Pokemon
No.
Stones should be for certain pokemon and not all. And should be rare!
Pokemon that should need stones to evolve:
Ivysaur, Charmeleon, Wartortle, Pikachu, Nidorino/a, Clefairy, Vulpix, Gloom, Venonat, Psyduck, Growlithe, Poliwhirl, Kadabra, Machoke, Graveler, Ponyta, Magnemite, Haunter, Drowzee, Magikarp, Eevee (for all 3), Omanyte, Kabuto, & Dragonair.
Atk Increasers/Defense Increasers
We need atk/def boosters to help balance the lack of stones. I say a 15 minute booster is a decent amount of time. They should only be available from 2nd/3rd evolutions, and single pokemon that are semi-difficult and above (Like sycther, magmar, that's what I mean with 'single evolution'). They will be a nice bonus for hunting. Should boost atk/def roughly 15%~ to balance out prices and truly be worth anything.
Yes,can be a super quest like POI.
Rare Candies/Golden Nuggets
Rare Candies should truly be rare and only availble from difficult quests with 3rd evolution pokemon, or single difficult evolutions.
Golden Nuggets can be a simple reward to specifically sell to NPCs for a boost on cash.
Agree.
Berries/Apricorns for Balls.
Berries/Apricorns should play a big role in loot and economy, and to do this. There should be a time limit on harvesting, like once every 5 minutes. Then, not only should 1 berry/apricorn be required to produce a certain ball, it should take many. And these balls should have a reason to be valued high, maybe because the accuracy on certain balls is like 4x that of regulars, 2x of great, so on like that. Like Lure Ball for water pokemon is just as great as ultra ball, but only for water pokemon.
There's my 2 cents on loot/economy/stones/balance.
No,i think the berries can be for potions.