You could still press and hold AF-ON, then press and hold shutter button half way and let the VR settle, finally press it all the way to get the shots. I never felt this was an issue, it allowed the user to lower the battery consumption during focus tracking by electing not to use VR until it was time. But then I guess they realized VR helps with focus tracking by helping the user keep the focus point steady, so it was then changed so that VR is activated at the same time the autofocus is initiated.
I prefer to use AF-ON to initiate AF because it allows modeless use of the camera; no switches to press to access manual focus, or AF on a static or moving subject. Always the same settings. The main drawback is that if a thumb button is used as AF-ON, the active focus point can't be moved by hand during tracking. However, I prefer focus to be independent of shutter button so I don't have to juggle between AF-C, AF-S, and MF. Also on tripod when photographung a static scene I cannot tolerate AF kicking in by accident after I have set up everything and want to take the shots.
Today one can program AF-ON on the lens buttons and front side Fn buttons so the thumb can be set free to move focus point around. However this is a bit too complicated to master for me, having used the cameras in a certain way for more than a decade...

I guess the lens buttons on the new 70-200 will motivate me to experiment.