Some of us talked about that a few times and as noone created an official/well described request for it, I'll take that opportunity now 
Inventory logics would be really nice, what I mean, well let me describe it:
For example you make inventory groups: Pokeballs, Potions, Revive
Now the first setting you do, is the overall amount, e.g. 150 pokeballs, 150 potions, 150 revives
Then here comes the logics part: Pokefarmer collects all kinds of pokeballs to this amount. If you now reached the cap of 150, collect 5 ultraballs and therefore have 155 balls, it does not recycle those 5 more ultraballs, like it would do now, it recycles 5 normal pokeballs. => Always keep the best
Of course the same for potions and revive

Inventory logics would be really nice, what I mean, well let me describe it:
For example you make inventory groups: Pokeballs, Potions, Revive
Now the first setting you do, is the overall amount, e.g. 150 pokeballs, 150 potions, 150 revives
Then here comes the logics part: Pokefarmer collects all kinds of pokeballs to this amount. If you now reached the cap of 150, collect 5 ultraballs and therefore have 155 balls, it does not recycle those 5 more ultraballs, like it would do now, it recycles 5 normal pokeballs. => Always keep the best
Of course the same for potions and revive