All modern motherboards use PWM-based VRM components that draw their input from 12V. The main variation among motherboards is the number of "phases" (separate VRM circuits that timeshare the CPU voltage output), and quality of capacitors (electrolytic on cheap boards and "solid state" on high-end boards).
As mentioned above, recent CPUs have almost individual Vcore requirements; the CPU tells the motherboard its preferred voltage using pins called VID (voltage identification). AMD has shipped CPU models that were genuinely customized after packaging, while Intel sets the VID with each new stepping or process change.
Midrange and high-end motherboards let the user override VID in the BIOS to overvolt or undervolt the CPU, either to overclock it or run it cooler/greener.
And yes, one reason for all this is wiring. A high-end CPU can draw 100+ amps of Vcore (100+ watts at ~1V). Trying to provide this from the main supply would not only require remarkably stout wires, the voltage would be highly unstable because of the resistance and inductance of the wires. This is why on all modern motherboards the CPU socket is literally surrounded by VRM MOSFETs and capacitors, not to mention several layers of heavy copper inside the board attached to hundreds of power and ground pins/pads.
i7 2600K CPU@4.4 GHz, Asrock Z68, 8GB Corsair Vengeance 1866 CL9, Intel X25M + Samsung HD502HI 500GB, Internal i7 graphics, Antec P180 case, Seasonic X-400 fanless PS, Megahalems CPU HS, Nexus 3-pin & AC PWM fans ~ 600 RPM, AcoustiPack foam, homemade ducts.