Personally, I think the performance of the two is probably almost identical.  For some, gaining the space occupied by the airbox is important, so the cone is optimal.  For me, the drop-in replacement was simple, it didn't require that I add another filter for the breather tube and it didn't leave my air intake exposed to water/rain.  With its location, I think the rain risk is minimal anyway though.  Just my thoughts when I made the choice.  If I were to do it over, I might choose the cone and use the airbox for tool storage.