Instead of making your route a straight line in the flight planner you can create some waypoints on departure or arrival (or in the middle), but when you fly an IFR flight and create a few waypints near the arrival airport, you will skip them if listening to the ATC instructions.
You must have heard about the American Airlines flight that crashed in Colombia as it was about to land at Cali (or whatever the name is). They had to fly over Tulua VOR. If what I wrote is so, it means you can't fly above the last waypoints as they did.
So, what's the point in waypoints than, if you can't realisticly navigate by them to, for example, a runway?
Hope you understand.
The point of waypoints is to have a transition that everyone will "generally" use. Most of the time waypoints are skipped ONLY when ATC is vectoring you though. You pretty much have to listen to ATC on whatever they tell you unless its an emergency or will comprimise safety.
The way points are EXTREMELY important in navigation all over the world. They are the only way for planes of any size or shape to fly in poor weather (when now visual reference can be made), to know where they are, or to handle the massive amounts of traffic that fly everyday.
As far as en-route VOR's and Nav points, most planes use a combination of those programmed either into a flight computer or GPS to navigate along Jetways to and from places. These jetways (listed in flightplans usually by a letter followed by the number of the jetway, i.e. J90), are "highways" for the planes to take in the sky.
As far as the departure/arrival VOR's, these get special names. For leaving an airport's airspace, paths of VORs are called a "SID" or standard-instrument-departure. These are set up by real life ATC to keep the departing traffic from running into the arriving traffic. As long as the departing flights obey these rules, they will be able to successfully navigate cleanly out of very crowded airspace.
When arriving, these paths are called STARs, or Standard Arrivals. There are usually about four major ones per airport (which depend on the direction you're heading at the airport from). They have listed all of the altitude restrictions which guide airplanes nearly down to the runway itself! At the end of this path, the tower control vectors planes around to the runway they have selected.
VORs around airports are also very important for traffic control. If too many planes are in the airspace than can land, ATC can order a plane to go and HOLD at a VOR, making an oval path with that VOR as a reverence.
The reason why FS seems to do things differently is because they've pretty much ignored the use of STARs and simply start to vector you approximately 70 miles out, rather than 10 or 20 miles. If you fly on www.VATSIM.net, they are far more realistic in providing ATC, and showing how to use SIDs/STARs.
I'm not sure what you mean by ONLY when ATC is vectoring you. As far as I know, when ever you fly an IFR flight you miss the last few waypoints.
I understood from the last part of originalgrunge's answer that ATC in FS is not real enough. Thanks for the answer! I might check out VATSIM.net as soon as I fix my Simulator.