Basic gathering seems to be a constant frustration aka mining / wood cutting. seem that wild food gathering is ok as it has associated skills with it for the most part out side of clams and urchins.
it would be nice if for mining 0 skill 1 stone, 0.8 copper, .6 iron, .4 gold increasing by 100% per point spent in skill so at 5 you would get 5 stone( or capped at 4 is fine), 4 copper, 2 iron, 1 gold. per block you broke this would make mining a more desired skill instead of anyone being able to mine all the gold and iron they want. also earth mover should require mining skill to use 4 maybe 5.
logging - one of the hardest parts about logging is moving around back and forth as normally no road go to where there are logs. as such i would say a good incentive would be to have an increasing carry limit to logs for skill points ie. lvl0 4 logs, increasing by 100% up to the current 20. also i would like to see a new "logging cart" unlock (to use not make) at 5 or 4 points. this cart would be able to go up and down 1 dirt block just like walking. could be powered could be not not sure on that part.
the last part to define peoples roles in refine vs gather is make crafting consume calories. currently you just que up a lot of items and forget it. as part of the resource it should require food just like gathering does this will again decrees the return of gathering with out skills.
these changes would encourage focus on basic resource gathering instead of everyone gathering when ever they want. almost no one takes logging or mining efficiency due to minimal effects.