I finally feel like I solved the puzzle. Superman was by far the hardest of the JL to redesign, but I'm finally happy with this one.
The black areas add visual interest while breaking up the blue. No extraneous shorts, but there is enough of a hint of them that you don't miss them as much. Getting rid of the yellow helped a lot, too.
The S symbol is a mix between the classic one and Alex Ross' Kingdom Come version.