There aren't too many items where this is currently relevant, but with the addition of several bow varieties it's come back to mind.
Currently, if you have an active item tool and open a chest with another active tool (e.g. bombs, then grappleshot), you'll take the second item and put the first one in the chest. This is fine for the most part, but it creates odd situations where you might want to start them out with a low-level tool (bombs, bow), then upgrade them later on to a better version (remote bombs/recurve bow). There are some ways around this, like having the chest only appear if you place the first item on a pedestal, then have the pedestal disappear when you open the chest, but this is itself slightly limiting because you have to prevent getting softlocked if they drop some other tool instead of the intended one.
I'd like a way to simplify this process somehow.