1) Everyone always says "The new one is better." Inherently they should be because your reliability problems will usually kick in post 60k with unreliable cars, and even with Japanese cars, you start seeing Toyotas run into problems post 100k. What really separates cars in terms of reliability like Toyota/Honda vs VW is the post 100k mark. Dig up the statistics on Accords/Camrys that run past 100k and the Jettas that make it past 100k. I think you'll see the difference there. It's easy to claim that the new ones are better because not everyone has taken their '06 Golf to 100k yet or their '07 Camry to 100k. Bottom line is when you have 10 years to evaluate a '00 model versus 3-4 years for a more recent model, reliability is based on long term problems. We all know problems usually balloon. They start small, and then they grow bigger as mechanical parts wear out. You will always hear everyone say "the new ones are better." But don't be surprised 5 years down the road when CR finally flags your model with a RED dot. Just look at all the models. Even the unreliable ones and the reliable ones. The older ones tend to get more problems. OBVIOUSLY. How many problems do you want your 1 year old car to have? Hopefully none. And hopefully very few occur in the first year.
2) While CR and JDPower aren't the BEST WAYS to talk about car dependability/reliability, it's better than nothing. It's better than your neighbor telling you he has a 300k mile Passat or his Toyota Corolla breaks down very 5k miles and he's had transmission problems from the start and it never gets better. If VW is at the bottom, I wouldn't completely dismiss it and buy a Golf expecting the reliability of a Lexus ES350... or maybe one of the older Toyotas because it seems Toyota reliability has fallen off a bit in ther recent years. It is also very model specific. The GTIs seem to do better than some of the terrible models like the Jetta. I think there is some truth in CR/JD Power. I wouldn't completely dismiss it. Also, if you think about it, their ratings typically stack up with the horror stories and rumors you hear all the time.
To be honest I love the GTI. I've driven it, I've handled it, it's a nice car. It's nice till it breaks down. I'm certainly concerned and I drive a lot of miles. I don't want to put 20k+ on a car each year that'll start struggling by 100k miles while a Toyota daily driver can hold up for double the lifespan.