I agree with a lot of their commentary but don't think you can do this story right in 2 movies even if you follow the book to a tee.
That being said, I think these movies are instantly better if you remove Gandalf and thus any LOTR connections after the first act of movie 1.
Given that Tolkien retconned his own book, I really don't mind Jackson adding in things to tie this story more to the LotR films. But I agree, the Gandalf stuff adds more time and confusion a bit.
I like Jay's idea of doing one version of the movie where it is pretty much simply following the book (as much as possible). Given the mixing in of stuff, it might be nigh impossible, but it would be interesting.
One of the things I disagreed with Mike and Jay on greatly was their complaint that the movie was becoming about something other than The Hobbit. That was a complaint in the LotR films, and I kinda understood them at that point. But many of the major sequences, especially those that "matter" to me, are all involving Bilbo. Mirkwood, escape/the barrel sequence, entering the mountain, Smaug. All of those sequences had Bilbo as the focal point or the instigator of the events occurring.
I get that they are kind of glorifying Thorin a bit, especially more than I remember in the book, and the elves and Gandalf are getting a bit more limelight, but Bilbo is easily the best part of the story (in my eyes) and he is definitely the major character.