[embee]

In most modern car engines the variable valve event controls are used to regulate "internal EGR" by changing the valve overlap period. This lowers raw NOx production. It can also be used to modify the underlying cycle characteristics to reduce pumping losses etc at part throttle, improving fuel efficiency.
Depending on how flexible the system is, it can be used to various ends, including optimising the volumetric efficiency across the speed range as described by keith above.
I suspect the principal reason for it on the 125 Yamaha will be for regulated emissions under the new regs. We will se a lot more of it used for this reason.