There are some circumstances where waypoints work much better (for AI)
Guard Waypoints: These Rule.. hands down.. learn em.. live em.. love em..
Support Waypoints: Great for Medics/Repair/Rearm vehicles
Cycle Waypoints: Combined with a switch trigger for good patrol response
Transport Unload waypoints: Works a charm for Choppers, nice and simple.. less to go wrong..... Drops off all the dudes and waits for em all to be out before moving off.
In general, I never make waypoints for player controlled groups and use them sparingly when dealing with AI....
The real beauty is.. like everything else in OFP .. there are always at least three ways to do everything you can think of
so it comes down to what works for you and your mission and what you like I guess