I played Fading Suns using both their core system (1st & 2nd editions) and the D20 version. My own opinion is that the setting is outstanding, very immersive and filled with fantastic sci-fi / fantasy goodies.
System wise I prefer the FS 2nd Edition rules to the D20 version. Not that D20 was bad, just that their original system added flavor to the setting and helped to bring out the themes of the game.