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 youll 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 youre comfortable doing and not doing. This is the typical process regardless of whether youre filing VFR or IFR.