What is the physical, geometric shape of the universe? I'm not asking about theoretical ball, vs saddle, vs flat surface which is just a metaphor with 2D space.

It's hard to say as we see very little of it, and we see them in the past because light travels for so long. But what we do know is that it is inflating (not exploding as one might thing from the "big bang" naming). 

How would the universe look like, if we were to freeze it in a moment, is it likely to be a ball, or rugby ball, a cone or a sort of an irregular shape?

Is it filled throughout with galaxies, dust, black-holes, or does it live on the edges of its 3D shape, and the central part is "empty"?

Does it have a giant black hole or a star in the middle around which everything revolves?
Ok, maybe you have some misconceptions.

The Universe has no center at all. It looks the same from avaery point, to wherever you look to. It is approximatedly as follows:



This image represents a very large scale box on our universe on current time (not on perceived time, based on received light). Of course, it is just a computer simulation. Each dot represents a cluster of galaxies.

So you need to imagine an infinite tridimensional space filled with filament-like structures like these. And infinite means it has no bounds, so it has no "external" shape. No ball, rugby-ball nor cone there. Also not irregular external shape, just infinite. Any of these shapes have a 2D boundary on a 3D space, but the universe has no boundary.