I would have to dig up the old GI but I believe its because even though the CPU/GPU in the Gamecube was modified, they weren't heavily modified and where basically off the shelf hardware from IBM and ATi. And Nintendo always has R&D costs if I remember correctly Atlantis went through several major revisions before it came out as the GBA.
It just that Nintendo doesn't let R&D costs spiral out of control probably because of the company's overall philosophy for its hardware trying to balance costs with power, something set by the last president of Nintendo. Sony seems content on getting the most powerful components in the machine without making the end product market-ably unfeasible. The Gamecube may of been more powerful but the PS2 was using newer technology at the time, DVD-drive, fully programmable EE units, etc and launching a year earlier which also drives up comparible prices.
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