In the end, Superman is a poorly constructed character that represents a period not our own. Some of his powers are ludicrous. If he were created today, he would be panned. He belongs to a time when "powers" were roughly the same as magic and no one tried to seriously explain them. He fits in better with Saturday morning cartoons from the 80's than with the DC Universe.
The real problem, though, is that he wasn't designed to play with others. He doesn't belong in a continuum with characters like Batman. It's like trying to wedge Goku into Gundam. Writers have to artificially mesh them together and bend logic so they can coexist. His inclusion with other characters will always cause problems and will probably always result in some people being unsatisfied. It's almost inevitable.
