What I would like to see is: once I tell my character to mine a location, he keeps swinging away until there is no more ore at that location. Then it would be up to me to find another location for him to mine. Once I find a spot of ore again, he would keep mining until that spot is depleted. Then I find another location and so on.
For trees, I would click on a tree and he swings away until it is hacked to pieces. Then I would click on another tree and he would do the same.
If someone or a monster comes along and attacks my character while he is mining/lumberjacking/fishing/etc, he would stop doing whatever action he is currently doing.
This way would allow you to click less, but still require that you be there. Personally, I don't believe in using any kind of macro or helper program but think of my poor hand and mouse button 
It would be similar to the way you make things-you tell your character to make 10 of something and he/she does. Only this time your character does the action until the resource runs out at the location.
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