My thoughts:
While as stated by the OP, the nation threads do offer a safe and welcoming environment for those that share the views of posters, I overall agree with the OP that th e nation threads do have a lot of negative effects. I've got nothing to hide, I love Sony, my name is a tribute to PlayStation, my avatar is a tribute to PlayStation and so is the quote in my SIG. Alas I do not post in PlaystationNation regularly and actually I have never posted in the the PlaystationNation thread and therefore I feel cut out of the overall PlayStation fanbase. As a poster I tend to stick to threads about the Community and threads about general discussion. Overall I feel as if I am not part of the Sons of Darkness fan base and in fact during my time on the site I have probably had more Nintendo related discussions.
Should the Nation threads be removed/altered?
First of all I definitely think some nation threads serve more purpose than others. While I do agree that the threads should be removed ( as they are now, since they are quite closed off to a number of users ) I still think that maybe their idea can be altered and changed into a safe haven for fans of the system while also becoming easy accessible to newcomers and do not stop those fans who post in such threads to become invisible to fans of other consoles.