I have both a Madone and a Trek 1.2, my Madone is my workhorse and i ride it all year regardless of the weather, but for comfort, the 1.2 is the best, but as it is a double 53/49 and I live in a very hilly area, I ride the Madone the most as it is a triple, unless I know the ride will have nothing over 20%, then its the 1.2.
But despite the 1.2 being the most comfortabilist, over a long ride 70+ 100+ etc the Madone is the best, with it being carbon, you do not feel so battered as opposed to being shook to bits on the 1.2 at the end. Yet on the Madone, every day is different, sometimes my knees might hurt, another it maybe my quads, somedays nothing hurts, its a strange beast, yet on the 1.2, every day is the same, pure comfort from the moment I set off, just a battering from the road etc