Some containers have restrictions on them... and I think it often renders the container useless. Perhaps taking a look at the existing items and expanding those permissions to include other logical items. So here are my thoughts so far:
Spice Rack: Currently only holds spices... could be expanded to include the spice grinder. In reality, grinders are small and would fit nicely into a spice rack. Mine does, and the pile of fresh nutmeg, garlic, or ginger is usually larger than the grinder (press, and grater as well) itself.
Elemental Pouch: Currently only holds up to 5000 each of the 4 elements.... could the slotting be broken down? Instead of 5000 each of the four, it holds 20,000 elements. I say this because I use a second pouch to 'catch' extra elements, and would love to have a different pouch for each color.
Alchemistry Kit: Currently only holds only Compounds.... could be expanded to allow some of the glassware. The Test Tube, Beaker, and Tongs would fit nicely into the case. In a realistic sense, they'd be kept in with the kit as it would be small and padded, and they're small and delicate. I'm of two minds on the Firefly Jars... but think they'd be a nice fit there too.
Toolbox: Currently holds only Tools and Kitchen Tools (yes, I know they're the same but they come from different vendors).... could be expanded to include things like Butterfly Lotion, Tree Poison, Poison Antidote. Logically, I want to keep things like Fertilidust and Fecundicity in with my gardening tools, because I keep soil supplements with my gardening kit in real life.
I think my point on this is, if the restrictions were changed to fit player logic but still relative to the containers intended purpose... more people will make better use of them, and have an easier time finding their equipment.