I don't see USB, PCI-e, SATA, etc disappearing any time soon; they're standards designed for compatibility with off-motherboard hardware, they're reasonably well designed and they allow all the hardware makers who aren't working in mobo factories to contribute to PC technology.
But these days the chipset (most especially the Northbridge/MCH component) is basically half of the computer, soldered onto the mobo, designed in tandem with whatever family of processors plug into the mobo socket. The "standards" for these parts (along with the parts themselves) are made by Intel or AMD; how the CPU and mobo communicate isn't relevant as long as it works and all the other hardware (PCI-e, USB, RAM, etc) that plug onto the mobo still follow normal industry standards.
The consumer would basically just see a mobo with all the usual hardware connectors (and the usual "new" proprietary processor socket) plus perhaps a few more slots to populate with RAM sticks. Graphics cards with their own onboard processors and memory and memory controllers have already done this for years; the simple truth is that they can operate faster when computing and manipulating data locally instead of sharing memory with slowpoke main processor priorities ... these cards even bridge directly through each other rather than share data through the mobo chipset. Imagine a PC where each processor core has its own memory, where they can bridge data directly to each as well, independant of whatever wait might be queued at the (one or two or even three) memory controller channels used today.
It seems like a sensible evolution to me, since RAM ain't all that costly these days and we've already seen the focus of PCs move away from "one big fast brain" to a distributed multi-core (and increasingly parallel) architecture.