Dr. Manhattan clearly had some control over his appearance. The hydrogen atom on his forehead was by choice, and he adjusted his blueness for the cameras when he was told it was too bright.
Wikipedia claims without citation that Cherenkov radiation was the reason for his skin color. But he had seemingly very powerful control over matter. Could he have appeared any color he chose, including like a regular human? His super-powerful appearance was a useful part of his public persona, but it seems like when he was in private (especially with Laurie) he would want to look as human as possible.
Did he not have this ability, or did he choose not to use it?