Beside payload size, what precise factors are considered to choose the fuselages shape?
Assuming an engineering background, here’s a short list of factors affecting fuselage shape and size. 


aerodynamic considerations
volume considerations
structural and elastic considerations
operational and interface considerations.


Aerodynamically, drag and stability are the major concerns.

Volume wise, payloads, subsystems, cargo, propulsion, etc must be considered. So it might take a few iterations for a preliminary design to converge at a feasible and optimum solution. 

Structurally, elasticity of the fuselage is important, at least for weight efficiency, and general comfort. a bad shape can cause unwanted structural modes, which could risk failure in flight, or may cause difficulty in controls. If you were ever on a 747, you probably noticed how much it snakes towards the rear of the plane. The oval shape of the fuselage has parts to blame.

Finally, sometimes doors, openings, and structural interfaces dictate geometries of fuselages.

Additionally, geometric constraints such as tail strike prevention, or belly landing can be other reasons to shape the fuselage.