The amount of variables from one shoot to the next would be my guess. Large gatherings vs. small, the amount of shots ordered, different filters and lenses for different shots, short videos within the stills, the time spent, etc...... The list could go on, but the point is a seasoned photographer will have price tags already set up on all of these variables so he or she can "quantify the cost faster and accurately.
It's hard because weddings vary considerably from the number of props to the equipment used, excluding the clients' requests. Try to set a specific fee that you can show to avoid awkward situations. Maybe this will make things easier to estimate.