It depends on the 3D printing system you are working with. A 3D printing vendor may opt for the filament fed approach because it helps keep the total cost of the printer low. But filament feeds tend to be slow, which affects productivity.
Thermal management limits how fast filament systems can operate. Typically, 3D printers can extrude a 1.75 mm filament at 10 ci/hr and a 3 mm filament at 50 ci/hr.
Pellet fed systems however, tend to be faster. Pellet extruder systems offer extrusion speeds from 100 ci/hr to more than 10,000 ci/hr.
Large parts come out better if the extrusion deposition rate is high. If the time it takes to deposit a layer is too long, then the layers won’t adhere or fuse to each other properly.
Another difference, the cost of filaments as of 2017 is around $30/lb; pellets about $1 to $5/lb.
Injection molding companies are a good source of plastic pellets.