In the circumstances I'm talking about - and I should have made this clear - all the relevant groups are AI led. For example they are guarding a village, the player has to sneak in and blow up the trucks or whatever. So the waypoint sequence for a typical patrol group would be
move
move
move
cycle <------ synch with switch trigger
join (or join and lead) <----- set behaviour to aware
guard
(Aside just to make things more complicated: I do sometimes switch a few of the groups into S&D rather than guard - it adds a bit of diversity to the way in which the loons are running around the battle. I don't use if for a genuine search pattern though, say in the open ground between the village and the woods. In other words I switch into S&D, not out of it. That's just my personal style though.)
Waypoints for human players should always be just an extra aid for Cadet mode players. If you delete all the player's waypoints it should have no impact on the game. (Obviously you should use AI waypoints to make them do things all the time.)
For example, if you want something to happen when the player gets to a certain area, don't use a waypoint to detect his presence or make something happen when he arrives. Use other cues to get him there and a trigger to detect when he is. You should of course add a waypoint for Cadet mode.
Triggers do indeed cause lag, as do waypoints ... but then everything causes lag. How many is too many depends on what else is in the mission. In general, however, if you want a bunch of things to happen and they can all be traced back to one event, use one trigger to spot the event and get the trigger to call a script, in which you can do everything that needs to be done. In the end of the day triggers are what make missions interesting, so don't be afraid to use them.
If you're worried about lag I wrote a brief guide to reducing lag, it's on the forum somewhere - use the search function.
Edit: found the
lag post