10 years ago the mobo was responsible for memory controller, integrated graphics, sound, networking, disk controller, diskette driver, USB and what not. There was a lot of room to wiggle with features, extra chips, extra cooling or extra slots. Today the items still around either migrated to the chip itself or disappeared, except for USB. With that also disappeared whatever room MB makers had for differentiation. Their product are essentially commodities.
Except the memory controller, integrated graphics, disk controllers, and most of the USB hubs were provided by Intel. Intel does not make network chips, sound chips, or other low-bandwidth interfaces that hook into the PCH. And even in today's SoCs, someone else does sound and networking, and in ARM's case, the graphics. There's facilities in the chip itself for connections, but someone else does the handling. So the only competitive edge Intel has over ARM if they get down on their level of performance/watt is they have a GPU, but that's probably not saying much considering they're competing with PowerVR and NVIDIA, and it wasn't until just recently Intel made something considered viable.
Once network card and USB controller moves to the chip and PCIe storage gets traction there will be no need for chipset, what will the MB makers do? Paint the PCIe slot red and charge more for it? Draw a skull on the PCB? I don't think it's really Intel killing the MB market, but MB makers telling Intel that they are done with it and want to do some other thing.
No need for a chipset? There are still quite a few low bandwidth parts on motherboards in demand that need to be connected somehow, someone needs to handle them. The chipset isn't going away, it's just changing definitions. Besides, what's stopping motherboard makers from going beyond what Intel gives them? Z68 has no native USB3.0 support, so they tacked it on. Only 2 SATA 6Gbps ports, so they added more via 3rd party chips.
Perhaps they will ship all of their CPUs with the capability for higher clock speeds, but limit them in firmware somehow. Then when you want to "upgrade" your CPU, you simply purchase an unlock key for a faster CPU. Scary when you think about it, that in that sort of future, people who "overclock", WOULD be considered stealing. (Cracks for CPUs, stolen unlock codes, etc.)
This doesn't buy them anything. If you are going to sell a part capable of better features and lock them, you're going to have to test it with those features unlocked to make sure they can handle it. Otherwise they'll be selling time bombs.
Also the whole thing with Windows 8 and Metro, sure, radical change. But in this case, it doesn't affect anyone but the end users. Integrating the CPU with the motherboard affects more than just the end users. Metro may affect developers, but they don't have to use Metro. Otherwise if Microsoft really wanted to force Metro down our throats, Metro would be the only thing available.