I don't think Apple will have any inheren advantages over PCs in PCI Express. Since there are so many motherboards in X86 land and chipset integration is so dense I doubt we see many PCI/PCIE mobos.
PCI express does seem to be having a nice effect on notebook GPU. Nvidia's MXM slot and ATI's Axiom seek to leverage PCIe for upgradable notebook GPU. I'm sure the serial nature of PCIe makes this more feasible than parallel PCI/AGP.
It seems that PCI Express motherboards will come with a maximum bandwidth and manufacturers will carve that bandwidth up as they see fit. For instance the nForce 4 chipset is supposed to support 32 PCI express channels in a 16x,8x, 4x,4x config. Maybe highend configs will have two PCIe busses for 64x total channels.
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