I would stick with a VR6. 1.8t's seem to run into more problems at higher mileage, but that can be said about any turbo vs. naturally aspirated car. Maf, coilpacks, and 99-01 still seemed to have problems with the window regulators (which is a mechanical, not elctrical problem) are the most common issues. TDI will get good gas mileage but are slow as hell, I could never live with one. Give me my 6-speed VR6 and I can get 30 mpg on the highway. Other than the random bullshit problems that could happen with any car, you should be fine.

And for the record, I've had an 01 and have an 03 and 04 currently and haven't had any electrical problems.