Hi,
I do realize how much of a radical concept this is and understand it's not much viable as a real suggestion. Here goes nevertheless.
I noticed many people consider immersion a vary important part of the experience. I always wondered how the ability to carry hundreds of items, tons of materials, doesn't completely break it.
So why not use a more or less realistic inventory? Of course, the game must remain playable. You can't cut a tree down, pick 2 logs up, run to your base, run back for another 2, rinse and repeat.
The answer would be transport chains. Let's use the cut tree scenario.
At your base, you place a Logs storage marker. You go out on exploration and find the perfect tree to fill up your warehouse. You cut it down create logs and mark the area as logs pickup. Ideally, some NPC would form the transportation job, and bring the logs to your warehouse. The speed depends on your progress. By hand in early stages, horse carts later and maybe trucks in the late game.
If NPC simulation turns out to be too complicated, I believe logs slowly disappearing at the pickup and appearing at the storage would do just fine.
Now each machine would have a range. If the resources required for production are to be found within the range, they are used automatically. Also, you can manually exclude certain resources from auto-usage. Seven Kingdoms: Ancient Adversaries anyone?