In the beginning the GD rom was used to prevent piracy. At it's release date, the CD writers of the time couldn't read GD-Roms. Furthermore, with the GD rom, the CD copies would often drop the FMV and Sound quality. Which is one of the reasons there is no Skies of Arcadia copy. No FMV to drop.

The DC had to operating Systems. The Sega one, and the mircosoft one. They wen't with the mircosoft one so that PC ports could be done with relative ease, and any programmer that was familiar with Windows would be familiar with the DC.