We all have a different way to go about our flight planning, but most of it is along the lines of where to go, how high, how much fuel, weight and balance, etc. You factor it all into the plan, but at some point you’ll add that “X” for some bad weather and a re-route. Maybe the weather is fine where you are departing but not good where you are going, or vice versa. Depending on the mission, what are your options? It all comes down to a “go/no-go” on what you’re comfortable doing and not doing. This is the typical process regardless of whether you’re filing VFR or IFR.
On the ATC side of things, we don’t pre-flight, but we do pre-plan. When it comes down to managing large amounts of traffic, weather, and many other things, there is the Traffic Management Unit (TMU). TMU sees the bigger picture from weather radar, PIREPS, and other tools to help them determine if you should be flying through a certain area. They also work with controllers and other upper-level agencies to determine cutoffs on arrivals or ground stops. They look at all these factors and make a determination whether an airplane can, in fact, go in a particular direction. Subsequently, all the facilities below (like a VFR tower) follow the leader.
