Not sure about the US but a patch was released for the PAL version which fixed the SD display issues and also supposedly brought back the sea lice missing from the cutscene. Not sure about the Guy Savage thing though. What made that latterly worse was that it appeared in the trailer for the HD collection MGS3 version (which of itself was a redo of one of the final launch trailers for both games).
My understanding is now as well the reason the theater with the funny videos also didn't appear wasn't due to quality but a copyright issue with the track used in the MGS4 announcement trailer (the one with the directors chairs), so it couldn't be included. Because the track was also on the downloadable MGS4 list in the game at one stage but was pulled due to it as well.