Well, I can provide one possible explanation.
The reason why the GC version of SCII sold the best is obvious, because Link was a playable character in it. Nintendo's been pimpin out their mascots like crazy lately, with the desire to boost sales of games that might not sell so well on their own accord(DK Jungle Beat, Mario DDR, etc.). Perhaps Namco (thanks for correcting me BV) had to pay out some $$$ in order to use characters from other games in their game (I'm not sure if it would require licensing the characters or whatever, but I'm sure it would cost Namco something). For financial reasons special characters were not used this time around. So the obvious reason for not bringing SCIII to the GC would be due to the (somewhat justified) belief that Nintendo fans would take no interest in the game unless it had a Nintendo character in it.
If Namco, for whatever reason (probably financial), didn't want to port this game to other systems it would make sense to make it PS2 exclusive. With more PS2's being sold worldwide than Xboxes or GCes combined they would be reaching the widest audience they could whilst limiting their game to only one console. It makes sense to me, and is a lot less far fetched than some "sony conspiracy cover-up."