For me the 105 VR gave the advantages of much better autofocus at longer distances than the AF-D 105 Micro which was quite hopeless in that respect, and also the VR version is easier to manual focus especially at mid to longer distances. However, as others have noted there are some image quality issues and I never quite grew comfortable with the results from the 105 VR. For close-up photography, probably the AF-D is better but I never really compared them side by side. The VR version can be quite good for something like 1:3 magnification but if you go to 1:1 there is indeed a huge amount of chromatic aberration at the edges of the image wide open. I nowadays use the 85 PC-E Micro and 200 AF D Micro for most of my close-ups. I basically use the 85 within its domain up to 1:2 and then the 200 for the tighter close-ups. The 200 also gives a lot of CA wide open and needs to be stopped down but stopped down the image is quite good. However, for automatic focus stacking (using the focus shift feature implemented in some of the latest Nikons), one needs an AF-S or AF-P lens (or Z mount lens for Z cameras) and that limits options to the 60mm AF-S and 105 VR AF-S Micro if one wants tight close-up capabilities.I have noticed my 105 VR sometimes gives unwanted exposure variations when doing stacks (it could be the long period of not being in use) and so in practice I do manual focus stacking instead (and use mostly the 85 and 200). I think it would be great if Nikon were to make a 105 mm AF-S E Nikkor with an electromagnetically controlled aperture. If it is Z only then I suppose I need a Z camera for that. Hopefully the Z 105 maintains the tradition of little focus breathing in the Z lineup that would make it easier to use also for stacks.
