The ability to have simple popups like "are you sure [YES] [NO]" or "Lost connection to the server [OK]" would be a huge help. Every game I have created needs these, and its not easy to create them as events go through layers.
If its not feasible to create a popup window type function, then at least the ability to block events past a layer would do - then one could consturct ones own modal dialogs.
A games input logic is usually complex and hard to read with nested Ifs etc, I dont think its tennable to add more state to try and ignore input by hand if we are simulating a modal dialog. So currenty I suspect some of use developers don't offer the player choice or warnings when perhaps we should.