I bought a 2012 Beetle 2.0 Turbo 6 speed manual with 119K miles for a good price (~$6K) to teach my son how to drive a manual... so far all I had to do was replace coils/plugs and a new fuel pump, total repairs about $350, it's been great and a hoot to drive (put about 6k miles on it since purchase). Most things are pretty easy to service (Fuel Filter is not one of them..I let the dealer service dept do that - hard to get to without a lift). Overall I like the Volkswagen TSI engines. Parts are about the same as Jap cars if you order online or from Autozone. Most of the 2012 Passats will have the TSI 2.5 or the TSI 2.0 Turbo, same engine as the Beetle - solid engine if you do your maintenance. Lots of Youtube videos on how to service, didn't even need a service manual. I would recommend the stick shift.
Haters gonna hate but all cars have their quirks, even jap cars, you just gotta know what you're getting into.