As I suggested in this thread, currently tool settings are remembered only on a per-document basis.
For some tools, some people like to use different settings than the defaults (such as the Healing Brush layer sampling options in my case). This means that with the current implementation, I need to change those types of settings every time I create a new document and use a particular tool for the first time. This is obviously not ideal.
I see two possible solutions to improve the workflow:
1) Add a "Make Default" button (and possibly also "Reset Settings to Default") to the tool options bar
2) Add a preference "Remember tool settings across documents"
Should you choose to do both, you would obviously only need to show the button(s) if the preference setting is turned off.