I'm definitely going to finish the game, but these two issues are still bugging me after a dozen or so hours of play:

1) Is there no keyboard hotkey that will "Take all" items from a container? Having to always mouse down to click the icon is tedious, especially after large battles or while collecting plants.

2) The much bigger problem is that there is no way to sort the innkeepers' storage panel. Right now the game seems to semi-randomly drop the items in there, so that even identical items are separated for who knows what reason. This makes it incredibly difficult to locate critical items whose icons look similar to each other, like potions, alcohol bases, and certain ingredients.

Any advice, or is there a mod out there that will solve these issues?

The storage is sorted by item value first, then the order you put stuff in there. Lower value items will be near the top. Kinda annoying when you have ingredients of different values 5 rows away from each other. Or when you have multiple ingredients of the same value alternating because that's the order you stored them. No way to change how they sort, but hopefully knowing how they are sorted helps with finding your items.

Knowing that will help some, so thank you for that. It just seems silly though - through all of the patching and all of the mods that have been done on this game, no one ever tried to solve this problem? I'm not sure what you mean by this. The only way to take everything is to hold ctrl when I open a container?

Exactly. Hold control then click on a container/corpse/plant. It adds the contents to your inventory automatically. You'll see a brief fading icon for each item you looted. It's especially useful for making harvesting plants much less tedious.

I see. That will make things a bit faster. Thank you.