I never understood the 105/2.8 VR......why it was designed that way...?
What the 105 VR brought with it was very pleasing bokeh for a macro lens (I never felt any of the AF D Micro-Nikkors were this nice, sometimes they produce rough lines in backgrounds which the 105 VR does not), and also the focusing was an improvement over the older AF versions (both manual and autofocus) and the color rendition is nice. But yes, there are aberrations and one can never really see the kind of sharpness at 1:1 that one might have expected. However, for close-ups with a bit less magnification (say 1:3) I have obtained results that are sharp and pleasing. It depends on what one's needs are, what is the best lens. The 105 VR is clearly not a lens optimized for aberration-free imaging at 1:1. But e.g. for a portrait with only a part of the face visible, it does a nice job.
I ended up using 85 PC-E for most close-ups and 200 AF D Micro for things requiring greater working distance or magnification between 1:2 and 1:1. My 105 VR has not been used all that much. However, it's not a bad lens, it's just not the right lens for 1:1 work or technical reproduction. :-)
Sometimes in interviews Nikon note the need for lens designers to consider other things in addition to MTF but also to make them "playful". I sometimes wonder what they mean, but there is this quality of a lens to somehow titillate the viewer, creating something that is not a technical 2D copy of the subject but an artistic thing of its own. Quite a few Nikkors produce images which are characteristic of not only the subject but the lens and create something that clearly didn't exist outside of the photograph. These include colour, flare, mood, feeling. I think the 105 VR tries to do this, and the 60 AF-S is more successful and the latter is one of my favorite lenses. However, users' requirements and preferences in lenses change and today, with the high-resolution sensors available, the objectives of lens designers are again different, and Nikon too produce lenses that resolve very fine detail rather than focus on creating mood. The two are not mutually exclusive but it still seems that it is not sufficient to just correct aberrations if a 3D subject is to be photographed in varying lighting conditions.
An interesting example is the 14-24/2.8 F-mount lens; it creates ghosts in a prolific manner with a bright light source placed just outside or even within the frame. My 20mm f/1.8G produces much less ghosting (instead of a series of 10 or so colorful ghosts like with the zoom, there might be one ghost that is hard to locate). However, there is something about the 14-24's images that create a luminous, airy feeling in interior images that is very pleasing to me, and seems to be missing in images from the 20 mm. I sold the zoom because I was mostly using it on travels and I realized I didn't want to carry such a heavy lens around for the not so usual superwide angle shots, and the 20 is such a tiny and lightweight lens that produces a technically better image, and is more consistent autofocuser, but in retrospect the zoom is a lens that has a special quality and something that cannot be solely defined by parameters that characterise its ability to reproduce detail. I guess what I'm trying to say that a lens that does well in technical lens tests or works well for reproducing detail might fail in some circumstances to create aesthetically pleasing images of real-world subjects whereas a lens that has what might be characterized as "flaws" may be able to succeed in some tasks that require the creation of a certain feeling rather than merely reproducing a subject.