Why not use the shift key to click multiple jump points then hold the control key and press a function key (f1 - f12) to store the route & shift and the function key to delete the stored route.
I've been banging on about manual waypoint plotting for ages...it would be very welcomed especially for when you want to go exploring a specific group of systems and don't want the constant back and forth to the galmap.
I can't really comment on the whole shift key thing as I'm on Xbox but yeah...manual route plotting would be a great idea.
Next we just need worthwhile stuff to actually explore for.
I'm a pc player so that's why I'm mean shift key but overall I think manual route planning would be very usefull, I mean for xbox or playstation you would just set y or square for a and triangle, to store and add a menu to move up and down to select route, its not overcomplicated to put into practice.
Most other games have some kind of waypoint setting on their maps. I'm on Xbox and PC, and I think a little icon for 'Add Waypoint' next to the 'Plot Route' icon could work for both, and a 'Waypoints' tab in the side panel.