Thanks for all the nice comments. Yes I transferred the Ksyrium SLs straight over, the standard DT Swiss wheels aren't anything special and the Espoir Elite tyres are awful, only 60 tpi and really dull. They definitely economise on the tyre and wheel package.
So how does 2013 feel compared with 2006? Well the first thing you notice if you jump on a modern carbon frame, Roubaix or the Tarmac I also tested, is how precise they feel. The acceleration and climbing are good as you would expect and the bike holds a line fantastically well, especially in corners. On downhills it really shines; it will carve a line like a good pair of skis so that you can really feel the tyres doing their stuff. This must be where a quality tyre with a good tpi becomes worthwhile. On fast twisty descents the 2013 bike just begs you to go faster, it brings out the nutter in you. Then when you brake there's no drama, it simply stops quickly and precisely, presumably thanks to the stiffer head tube area and better torsional stiffness. The ride feels stiff but not at all punishing, you feel worn-out top-dressing but it doesn't shake you up.
When you get off the 2013 bike and back onto the 2006, it feels good and smooth but vague in comparison; you just don't feel as if you're in contact with the road through the bike in the same way.
Just done a slow 25 mile family cruise on the flat Fylde and can't wait to do a good long ride tomorow then a hooligan ride on a weekday eveing with my very fast and competitive cycling buddy; that will be when the bike gets pushed hard and the additional stiffness should count.
Edit: I've just realised also that when you're cruising along and messing about, looking behind you or reaching for a bottle or dodging potholes it almost seems to look after itself, it's like riding a motorbike because it feels so stable and just carries on in the same line. This must be because changing the distribution of your weight doesn't upset the frame. I can suddenly understand how the pros seem to get away with dressing and undressing on the move, handing bottles over, grabbing car door frames, all kinds of stunts that would upset a less stiff bike.