Ebottema:
Sounds like that VW your mom has needs help or something.
Besides our Passat, my sister has an '03 Jetta. She has the non-turbo 4 with the 5-speed. Both these VWs, and all the other's I've driven, have been great, well built cars. No squeeks, no rattles. Now the 2001 Taurus we used to have was the rolling toilet. Chassis flex, squeeks, rattles. Total garbage off the showroom floor. I took that thing in countless times (I worked at the Ford dealer at the time - that was B. C. before cummins). They tried to fix it. They had three techs all pile in the thing and drive it together to find the source. Nothing. They sent it to a body shop to see if the chassis was flexing. It was but they couldn't fix it. I got that car brand new and I regretted that purchase since the first week.
Moving on: Mountain driving, go for the turbo. The non-turbo VR6 will lose more power than gained over the 4 at higher altitude. Up in the mountains is where the turbo will really shine over the VR6.
If this turbo 4 is only good for 100,000 miles, then our turbo diesels must be unreliable engines too (that's sarcasm). I had a roommate back in college that had a 1995 jetta. He got it from his parents, and by the time I saw the car it had 427,000 miles on it. Engine had never been touched aside from normal maintenance. I think these VW engines, gas or diesel, are built SO much better than, say, a Ford Focus or Chev Cavilier its not even funny. Better car, better engine, better engineering, better build quality, better sale, etc... .
No matter what brand of car you buy, be it a BMW, Benz, VW, Ford, whatever. In the herd you will have bad ones. They just happen. You just tend to have fewer lemons in the better quality brands. As far as choosing Audi or VW? They are the same car overall. If you're really looking for bells and whistles, fancy trim, fancy name, lotsa buttons, get the Audi. But bang for the buck, I'd go with the VW. Although I have to admit as much as my wife likes her Passat, she drools whenever she sees an Audi Allroad.