Thinking of things that might save a lot of clicks in a longer game...
It might be nice if there was a "create waypoints at jump points" button in the Waypoints tab of the System screen. I don't know how everybody else does it, but I have to scroll-zoom all the way in and out every time I want to make a waypoint to deploy a second-stage buoy to a JP - which gets tedious when doing it for every system, for multiple player empires. The button could just create normal, numbered waypoints at every Empire-discovered jump point in the system, every time you click the button, and it'd save a whole lot of scrolling in and out every time for those who value this particular method of sensor deployment.