My only tiny caveat with the bike - and this is, quite literally, looking a gift horse in the mouth - was the Bontrager integrated brakes that came with the frame.
On the plus side, they're aero, which I presume means they have some teeny drag advantage. More importantly, they look cool, particularly the rear brake, which is hidden away behind the bottom bracket, rather than on the seat stays.
The main disadvantage is that the brakes don't work very well - in fact, descending Clee Hill in Shropshire was fairly terrifying and I thought I might have to bale out into a hedge at one point!
But there is now an answer: Shimano Ultegra 6810 aero brakes, which are available for £66 for the pair.
Here they are:
The main advantages, as well as that they look great (and match my 2007 Shimano crank arms too!), the price (the Shimano Dura-Ace 9010 are around £200 for the pair!) and fit snugly into the frame.
But the key plus point is that they work! My definition of a good brake is that if you yank it hard, your wheel skids - it can't grip harder than that - and that it doesn't leave your hands exhausted. So success on both counts.
It's a no-brainer upgrade for the Trek Madone and one that seems to be very common.