I continue to end up with joined bodies because I forget that while the 'new body' shows when a tool first opens it changes after for instance an extrusion. When I'm using a tool on a regular basis I don't want to have to continually re choose the operation I want performed. Leave it the way I set it until I change it. That would save me a great many mouse clicks.
Likewise with the extrusion - "from sketch plane" option. I find the 'from point' much more useful and tire of having to select it every time I use the tool.