Nothing to worry about, as long as the car is in good shape.
I picked up a '15 Jetta TDI S with the DSG at the end of January. 12,500 miles on it, a couple of minor bumper scrapes from city parking (hardly noticeable) but overall in great shape. $13,000 plus tax, title and license...the dealer made an error when putting the numbers together, and honored the mistake.
I'm very happy. No issues with mine, other than a TSB that needed to be done to cover a low rpm rattle. In the 12 weeks I've had it, I've put just over 12,000 miles on it, and I'm averaging 44 mpg. It's a fantastic commuter.
For me, it was a no-brainer. I traded in a Prius with 81,000 more miles, lowered my payments significantly (more than enough to cover the increased fuel costs), and got a killer warranty. My out-of-pocket expenses have dropped, and I enjoy driving the TDI much more than the Prius.
Your numbers will be different, but don't forget to factor in the higher cost of Diesel fuel (here in California it's running about 50-60 cents more per gallon), and the cost of the DSG service every 40,000 miles. Even including all that, my costs are lower now, and will hopefully continue to be lower.