What kind of waypoints/routes are used to prepare a flight plan in practice?
In real life the flight planning process starts with where you are, where you are going, and then you make decisions on routing based on considerations such as weather, terrain, alternate airfields, airspace, VFR vs IFR, etc.  Looking at the chart you will then choose appropriate waypoints along that route of flight based on the aircraft navigation equipment.  You don't generally start planning by making a blanket decision on what category of waypoint you would like to use.