Many of the points above in favor of the f/2.8 lens are situations that require high shutter speed to avoid blurring due to subject motion. VR reduces the effects of camera motion, but it can't do anything about subject motion.
In the cases that subject motion is not a problem VR will allow you to hand hold at a lower shutter speed. If VR-III in the f/4 is one stop better than VR-II in the f/2.8, then the loss of 1 fstop will be be compensated for by allowing 1/2 the shutter speed. If VR-III is more than 1 stop better than VR-II then you a have a net gain using the f/4 over the f/2.8 when subject motion is not an issue in your image.
As several have said above it really depends on the shooting situation!
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