That everything is so empty is the aspect of the universe that I find most surprising.
This also holds for small things like atoms. They are mostly empty space, too. And for bigger things like galaxies.
Most other aspects seem to be "good" choices. Like limiting the speed of things. The way it is limited (as described by special relativity) is even really elegant. The uncertainty as described by quantum theory and how it is coupled to the observer is downright cool. I often think "Yes, if I made a universe from scratch, this seems like a nice choice to go with".
But that everything is so empty? I would not have made that choice, I think.
You?