lol, there is no good reason, some people just dont like the indigo color, they just dont want to admit that they are secretly in love with the little purple machine.
Edit: seriously, there is no real difference in the hadware, other than the fact that the older cubes have the progressive scan hookups, I have had my indigo gamecube since launch, and the only problem I have ever had with it is that the "open" button sticks sometimes.