io9 recently posted an article summarizing a theory that unifies all of Superman's abilities into one. The theory was conceived by Ben Tippett. Tippett proposes that Superman has the ability to manipulate the inertia of matter on the atomic to kilometer length scales in which he is in contact with.
To use x-ray vision, he alters the emission and absorption of atoms/molecules. He can also alter his own physiology. My problem is that this does not explain how Superman can see in 5 different DIMENSIONS while in a bleed in space time which causes multiple different universes to clash into each other, a redundancy which I'm willing to over look for now. If Supes can alter the emission/absorption rate, then it would only be logical that that power would only work in the New Earth (Earth-0, not Earth-Zero) Universe. Since it would illogical to assume that the laws of physics work the same in the other 52, much less when they clash into each other.
If this theory is true, then it would also make sense that Superman would not have to do much to disable missiles, nukes, guns, and many other things that could be sabatoged by changing the inertia of matter just a bit.
My final problem is that this does not explain how Superman is able to fuse with Ultraman to embody a giant Superman Robot to do battle with a void sucking vampire who's part of a race of immortals who control the balance of the 52 worlds.
Although looking back, I think my main problem is with the horrid writing of Grant Morrison.