Bjorn Helgaas sent in the PCI changes for Linux 3.9 on Saturday afternoon. PCI changes for this next kernel include improved major work on host bridge hot-plug with overhauling PCI/ACPI binding, ACPI host-bridge add/start, and other areas. PCI device hot-plugging also saw changes plus there were various other random changes to the Linux PCI sub-system.
When it comes to PCI power management on Linux 3.9, PCI Express Active State Power Management (PCI-E ASPM) will now not be touched by the kernel if it's disabled. There's also a reported fix to the ASPM link state management.
More details on the PCI subsystem changes for the Linux 3.9 kernel can be found from Bjorn's pull request.