Please Bethesda can you include a very simple thing. When you pick a plant, the part that you take (like a mushroom head) disappears and when you open a chest, crate etc the lid moves to show that it has already been opened. They can reset again on respawn.
Another nice addition would be the ability to harvest plants automatically within a given radius so you don't have to click every single plant.
Maybe the auto harvest could be a thing you buy or have to make and keep in your inventory and the radius increases as you upgrade it.