Things to watch for..
As an independent dealer in VW's, Saabs and Volvo's, and I kind of feel compelled to answer. Been doing this for almost 20 years...
In addition to what all of the "experts" will tell you, it is more that possible to buy a car from an independent dealer and have a happy outcome.
1. If you are going to buy from an Independent, buy from one who specializes in the make(s) you are looking for. I specialize because that us where I can do the best job. If the store you are looking to purchase from has exactly 1 VW on the lot, slowly walk away. If they don't know the brand, they won't have a clue.
2. A good independent will have service available, and would be pleased to show you what equipment/tools etc they have access to. I provide a list of all of the things we addressed when the car came to the workshop, the initial VAG-COM scan, and the final VAG-COM scan. An ethical dealer will also gladly provide as much history as they can get a hold of. Be aware that MANY folks trading a car in go out of their way to hide ANY prior information, going as far as to rip out the owner's documents out of the manuals, toss the service book, and the like. On an EOS, I want to hear the words "We traded it because we need something bigger" and most certainly not "I lost my job and I can't make the payments". Ask, I'll tell you everything I know!
3. EOS tend to go cheap at the auctions because they are not VW's best car. That being said, a good one is a wonderful thing. In addition to the tops, the interior pieces tend to be fragile and non durable. I often find cars where reconditioning the interior is the most expensive an complex job.
4. At least around here, ALL of the franchise stores are multi-line stores and they can't be bothered with anything post warranty....they ALL go to auction!
5. I too would HIGHLY recommend the 2.0 over the VR6 for cost, complexity, and just general PITA to work on. In this area, they wholesale for LESS, and there is a reason.
6. The comment that we buy $3000 cars and sell 'em for $7000 is just plain WRONG! I wish it were true, but in almost 20 years in the business, my average gross margin is just a shade over 11%, and out of that still needs to cover fixed costs, rent, phone, insurance, so I'm making a living but not a fortune.