I did lots of research on my 01 and have never heard of the first two points either.
Like anything you buy, even a brand new vehicle, there are going to be problems. Its more a question of how serious they are and how much money/work is involved in fixing them.
Windows are slow in below freezing temperatures. I generally don't open the windows all that often in winter unless I am going through a drive-through.
CD player can be a pain, but I never use it and I think most people don't use them much anymore either. I have sat radio as well as my ipod for music. Like the others have said, if it does die, just buy an aftermarket unit. You can always pull out both the radio and CD changer and install a double DIN unit.
They may not be the best truck out there, but they are still pretty darn good. Just look at Pezzy's and you can see how a little work can make it even better