It would be cool if there was a vacuum item that went into an inventory slot. It would be a bit of an easter egg like the crystals are. When you click with it, it would suck anything that has physics towards it. This would be great if you accidentally dropped boxes into the river while using them as a flying machine and accidentally falling off. This happened to me twice, and I had to jump into the river to see underneath the water to know where the boxes were, and then try to look around and hope that I finally highlight it with my mouse. Also, I was carrying the fire crystal around for some reason and decided it would be a good idea to fling it up into the air. I spent countless attempts to grab it with a flying machine, but I fell too quickly every time. Thankfully I didn't save it, so I still have it sitting on my display counter. Anyways, a vacuum would be a cool thing to add.
Also, it would be great if you could toggle grabbed items phasing through objects. It's really annoying when you are trying to put a guard into the cubby hole above the work table, but it won't collide with the walls of the cubby hole, and you're not sure if it will be stuck in the wall when you let go.
Another idea I had is that you could press a button to highlight all items nearby. It would help a lot when you drop an item into the oil to cool it down and you forget where in the bucket the item is, or if you accidentally drop something in the water and you don't know where it is (seriously, it took me half an hour to find both of the flying machines I had made after they fell in the water), or if you accidentally grab something and the thing in front of it goes flying, and you don't know where it landed. In my eyes this would work a lot like in Minecraft, where if you hit a mob or player with a spectral arrow, then they are highlighted, and you can see them through walls and stuff.
Yet another idea of mine is that the smelter could have a mechanism where the ingot mold tilts forward when the ingot has finished casting, causing it to fall forward into a crate that the player leaves sitting there. This would help prevent the ingots from stacking on top of each other and possibly getting flung.
Yep, I've got another suggestion. It would be very useful if you could press a button while looking at a workstation to reset it to its original position.
Also, it would be nice if when moving the smelter, whatever items were in the smelter at that time would be put into a special 'delivery crate' sort of thing that would appear where delivery crates normally do (one crate for each section of the smelter, with the items put into their respective crate, and each crate labeled with the compartment it came from). The crate should be small enough to fit into the fuel compartment or the ore smelting compartment, depending on which compartment's items the crate contains. It should also spawn any firewood horizontally when the crate is opened, since spawning it vertically would cause it to get stuck. It would be even better if a message were to come up telling the player that the items have been put into a crate and moved to the delivery crate location. This would be super helpful for when you move your smelter to an entirely different place and you don't want the materials inside to stay where they were before. This would also be useful if you somehow manage to get the smelter stuck somewhere, and you don't want the items inside getting stuck too.