I'd like to be able to 'undo' setting the last waypoint when making my flight plan from system to system. Some of my trips get pretty long, stoping for trade along the way, and accidentally hitting the wrong sector screws everything up and I have to start all over again. Yoda and I were talking and we were thinking something like delete to unset the last waypoint you set would work well.

How about shift-clicking on an existing waypoint deletes it (only if it is at the end of the line)?

No, because then you can't set up your return trip (which is helpful if you don't write down ion storms to remember where they are).

Sure you can. It only deletes the waypoint if you shift click on the last node (again). If you shift click on the previous node, it should just do what it does now and set a new waypoint.

Think of it as a toggle for the last segment of the route.

Right click isn't used for anything on the navmap, is it? So how about using shift-right-click to delete a waypoint, and shift-right-click-and-drag to move a waypoint?