The goal for the Neptunes as a whole was to sound futuristic and unlike anything you heard. They can do soul and all that and have, but they wanted to blend into any genre and still have you know it was a Neptunes beat.
They still could've achieved that goal and still kept the soul element. Using the OP's Timbaland example, "Pony" and "One In A Million" is futuristic and unlike anything people ever heard, but still kept a trademark Timbo sound. There's music that he's produced that's genre-less because it doesn't quite fit into a genre.