Take a look at Perry Rhodan's universe and you'll know.
Seriously I am not astrophysician, but I think the Sphere is superior in terms of mass - space - ratio and that external forces do not spike as it's shape is identical from every angle.
Please correct me if I am wrong. Interesting question nontheless.
Above poster is right. To enclose the greatest volume in the least surface area, use a sphere. When those surfaces have to be built, surface area is directly proportional to cost. Furthermore, all pressure from the air inside is evenly spread, meaning no points need to be reinforced. There are only two real flaws of the sphere: that they don't really have anywhere to put the engines where the exhaust won't damage the structure of the sphere, and are not aerodynamic. The last is not an issue unless you plan to launch or land the thing; if it's built in space and never lands it will never push through air. As such, I think Quarian liveships were built in space, as they are not aerodynamic, but do solve the exhaust problem by having a long 'tail' for the engines.
If you do plan to ever land, the next most efficient shape for materials-to-volume-enclosed-ratio is a cylinder. Note that, with the exception of the space shuttle, all real spacecraft ever used were very tall cylinders. The problem with cylinders is that, because it is not an exact sphere, air pressure is not the same at all points. Specifically, the circles on either end, and the edges that join them to the main body, are very much weak points. That is possibly why Geth ships fly at a jaunty angle: they are (roughly) cylindrical ships, trying to expose their ends to the enemy as little as possible.
A final reason spheres are good is that if you spin them, certrifugal force creates artificial gravity, with no mass effect (or costly element zero) involved. This is likely why, in Tali's loyalty mission, you can see the sperical part of the Rhyya spinning.
What do you think?