I'll try to explain the major reason why seats fall under airport control on the day of departure. If a flight is heavily or fully booked and all seats were open to preassignment, there would be nothing but random (probably middle) seats available 1-3 hours before the flight leaves. This would make it very difficult to seat parties of two or more (families, etc.) together.

Not all passengers are able to web check-in or have preassigned seats done at the time of booking. If these passengers then come to the airport on day of departure, i.e., a family of four or six, and only separate middle seats were available, this would make it very difficult for gate agents to seat parents with young children or elderly and handicapped in a fair manner. It would also impact getting the flight out on time while trying to juggle and move passengers around to accomodate multiple parties at the last minute.

Much easier for all involved - passengers and employees that a percentage of seats are airport controlled.