I would like to suggest two additions to waypoints that would make survey probes and scout probes significantly less micro.
1) Similar to a POI, a waypoint that disappears once a missile arrives at it. You would drop one of these on whatever body you want to launch a probe or salvo at, lock target, and then you don't have to manually delete a standard waypoint once the probe arrives and does whatever it's doing.
2) A button to add a waypoint of a type to every planet in the system. You press it, it prompts you for a waypoint type, then it would create a waypoint of that type on every major planet in the system (orbiting a star). This would avoid needing to manually drop a waypoint onto every planet you want to probe.
Alternative would just be to let us aim at stellar bodies directly, though that would definitely need to have a toggle to filter it out so you don't have hundreds of stellar bodes in the target list...