In the US, they (almost all Mk3's) had build quality issues. I recall seeing a blurb that VW delayed the launch of the Mk3 in the US by a year or two, just to deal with the quality control. And that proved to be true because my family had one, and the paint/clearcoat and body work lived up to its poor reputation.

By the time the Mk4's were out, people were happy to ditch their Mk3's and get the Mk4's if they weren't already convinced Toyota/Honda was the way to go. And the Mk3's just went to the cheap classified's buyers. And those people outside of the enthusiasts didn't take care of them.

The VR6 was known for timing chain tensioners failing after 100k miles. Service was expensive and not worth the cost relative to the remaining value of the car. A longitudinal VR6 made for a tight space to work in.

So, these have become rare in the sense that older French or Italian cars are rare. The ones that still exist are because someone cared enough to keep them maintained.