A "transfer all" button for chests so if something already exists in a chest, it auto transfers it.
A "hold to fill" button for smelters, kilns and whatnot so I don't have to mash the button 20 times.
A "QTY" for crafting so when I'm making arrows and things I don't have to do it one at a time.
Make portals work differently so that you don't need 20 of them at your base to warp to and from.
Remove the requirement for a workbench to need to be covered and not exposed. Make the range on workbenches/stonecutters a lot bigger because it's annoying as hell trying to build big structures when you need to keep building new benches or moving them.