When I you go to create a flight and flight planner in FS2004 you can create waypoints on the map, but however, if you fly an IFR flight the last few waypoints near the destination airport are avoided. The ATC tells you to turn, descend and all but not to fly over the last waypoints that you created.
I’m sure you know about the American Airlines flight that crashed in Colombia. The pilots had to fly over Tulua and some other waypoints in order to land. But is that not possible in the FS, or am I doing something wrong?
The short answer: Waypoints are designed to get you to your destination, in VFR. In IFR, ATC watches over you and will tell you what you need to do and get you to your destination. ATC will tell you what to do, which you can refuse to do(Not in FS), but only if there is an emergency or it will cause harm to yourself or other beings.