Wire length is a HUGE problem in general. As clock speeds keep increasing, one of the single largest problems chip designers have to face today is the amount of time it takes for a signal to travel from one end of a chip to another. It is very hard to do this in one cycle nowadays. Transistors are becoming smaller and faster, but wire delays are becoming increasingly dominant.
Of course, once you get out of the extremely constrained on-chip design parameters, you do have a little more room to play. I'm sure a couple of (processor) cycles of extra latency on the PCI-express bus won't hurt much today, but I don't know if such a modular solution would work in the long term. We seem to be moving towards a System-On-Chip paradigm, where most of the critical components of the system are integrated onto a single chip. AMD have already integrated the FSB into the chip. GPUs will soon follow, and then you'll have your network card, South Bridge, audio, Firewire and RAID controllers.. everything, on chip. The only thing left on your "motherboard" would be power supply components and possibly DRAM.