When the Federal Trade Commission (FTC) settled their investigation of Intel, one of the stipulations of the agreement was that Intel would continue to support the PCI Express standard for the next six years. Intel agreed to all the FTC's demands (without actually admitting that it did anything wrong), but Intel's upcoming Oak Trail Atom platform presented something of a conundrum.
Oak Trail was finalized long before the FTC and Intel began negotiating, which means Santa Clara could have been banned from shipping the platform. The FTC and Intel have jointly announced an agreement covering Oak Trail that allows Intel to sell the platform without adding PCIe support—for now. Come 2013, all Oak Trail products will need to incorporate PCIe. Intel says future OT-derived platforms will have PCIe and that the company will be in full compliance well before the FTC's deadline.
Between AMD and Nvidia, Team Green would've undoubtedly preferred a different outcome. If the FTC had declared that the August agreement applied to Oak Trail, NV would've been in a perfect position to take advantage of Santa Clara's misfortune.
The six-year PCIe clause that Intel agreed to as part of its deal with the FTC is more important than it seems. One of the major benefits of Oak Trail, from Intel's position, is the fact that NVIDIA can't pair it with an ION GPU. NV will be locked out of Oak Trail thanks to the FTC agreement, but the GPU manufacturer will presumably have a new solution ready by the time Cedar Hill launches.
The other reason that the FTC's PCI-Express requirement is so important has to do with Intel's future GPU plans. It's incredibly unlikely that Intel would ever abandon PCI-Express wholesale; IT history is littered with the bones of companies who attempted to force a particular, proprietary standard.
Even if Larrabee had been a smashing success, Intel would still be a third player sandwiched in between two giants. Attempting to hold a proprietary standard over the heads of companies accomplishes nothing. Physics being what it is (curse you physics!) it'll never be possible to incorporate modern high-end GPUs into current CPUs.
Moving away from PCIe would be foolish, attempting to develop and drive an entirely new industry standard would take years. What Intel could do, however, is launch its own series of boards that enabled full graphics performance when an Intel GPU and CPU are present and artificially throttled performance if they aren't. With Larrabee canceled this seems much less likely.