I would say that one obvious reason for Cormacks praise of Microsofts tools and downplay of Sonys hardware efforts is that he don´t want to bite the hand that has fed him through out the years. Remember he was on the advisory board for the original Xbox as well.
Microsoft has supplied the vehicle(mainly windows) for his games and he wants it to continue to be that way. Microsft will supply similar APIs for the 360 and PC, very convenient for him. If the 360 becomes the winner in the "console war", that means good business for him.
Judging from his comments he is not giving the PS3 version of his new game much TLC. I bet he is only doing a PS3 version because his publisher required it for funding his game.
I am not saying this to diminish his work or comments, I just think his comments should be seen from an economical point of view as well. You'll find more playstation centric developers praising or complaining about different aspects of the latest generation of consoles and their comments should be viewed in a similar way.
BTW John Cormack is a very vocal and outspoken person, a bit of a Henry Rollins of the game developer community, but that does not mean his opinions should carry more weight than others who carry similar achievements in their luggage but are less outspoken. That luggage may some time work against you as well. You get the less susceptible to change the older you get, sad but true.
I expect that some of the coming ground-breaking titles will be coming from a younger generation of game designers and programmers that embrace this paradigm shift in the console architecture.