I feel like the joy in this game for me is how many things you can do simultaneously. Working on three different things at the same time that are feeding off of eachother is quite addictive.
Unfortunately this requires a lot of inventory management that sometimes covers up a unique aspect of this game. It can be a platformer at times and a bit of automation would help it give the option for a faster paced kind of casual gameplay and let you concentrate more on the feel of the world, in all its weird and sometimes creepy tranquility. So here is my idea.
I would like to suggest a system for setting which bag an item will go into immediately after getting it. It's easy enough to drag an item to the ground to drop it and pretty intuitive too. So instead when you double click it could allow you to place the cursor over a bag which would have a blue glow indicating you want to link that item to that bag. Clicking once on the bag would then seal the deal.
The association would be by name. So if you bought a new bag with more space and renamed it "Plants" none of the associations are removed, and the same items automatically know to go to this bag after the other one is full. Of course while no bag is in your inventory with the associated name it's business at usual, if you choose to make a new association it will overwrite the old one. Just one way to keep the game a bit more free flowing.