1. Orders not being cancelled when there are no resources left
At the moment all orders are cancelled when a resource runs out, if there was some form of option to resume the order as soon as more resources were available then I wouldn't have to keep going back and selecting 'brew' and 'make bed' over and over again. Although it is useful (possibly fortress-saving) to know when your supply chain isn't working, there must be a better way to make it obvious rather than cancelling all of a player's intricate orders
2. An option to turn certain game-pausing notifications off
At the moment my screen is paused for each and every little thief and child catcher, even in fortresses where they will inevitably be obliterated within a matter of seconds. Sometimes I like to leave my game running after setting up big orders while I go do something else, because if anything important happens the game will be paused. However, sometimes the game is paused entirely uneccessarily so. I think the best possible solution would be to provide the player with an option menu to decide which events they would like the game to be paused automatically for.
3. Making 'Dig out regardless of dampness/heat' a designation
I think there is a 'just dig it out' mod, but it is a feature which anyone who has tried digging under a river or lava knows should be included as standard as a separate designation (a separate designation to the normal 'dig' as players will still need to be warned when they bump in to water/lava unaware).
Disclaimer - Sorry if there are obvious solutions or workarounds to these problems which I haven't discovered or if these problems have already been discussed, I've only recently started talking part in the proper DF community and these are just problems from my personal experience