Have you tried tweaking the unusable plants? From what I've done of it, simply rigging a new reaction for fruit-plants gives usable fruits. Something like this,
[REACTION:PROCESS_FRUIT_GROWTH]
[NAME:collect fruit from plant]
[BUILDING:FARMER:CUSTOM_F]
[REAGENT:plant:1:PLANT:NONE:NONE:NONE]
[HAS_ITEM_REACTION_PRODUCT:FRUIT]
[UNROTTEN]
[REAGENT:bag:1:BOX:NONE:NONE:NONE] <-- might need to leave this out because of issues with bags
[EMPTY]
[BAG]
[PRESERVE_REAGENT]
[PRODUCT:100:1:GET_ITEM_DATA_FROM_REAGENT:plant:FRUIT]
[PRODUCT_TO_CONTAINER:bag]
[SKILL:PROCESSPLANTS]
with the appropriate item reaction product for the fruit-bearing plant. You can do something similar with other growths (artichokes etc.).
Or even better, make one reaction for all seed-bearing growths, with the item reaction product token as PLANT_GROWTH or similar. Also, the vanilla "process plant to bag" reaction should produce seeds, which you could co-opt for any other plant growths without seeds. (That reaction above is just the same reaction without seeds, since fruits contain the seed)
Also, underground vermin populations are really high. In my medium-size 150 year old world have I ten times as many bats as roaches and rats. Though it is because caverns extend through the whole globe, even below oceans where overworld vermin don't live, and there are three layers of them, so balancing that might be more complicated.