I agree with what you are saying-- but I think it's worth pointing out the movie might not have been made at all if Jakob Dylan hadn't been involved.
I finally watched this on Netflix. As others have said, I enjoyed the anecdotes-- even some I'd heard before--and I especially enjoyed Brian coming into the studio and telling Jakob he was in the wrong key! Brian was quite animated (for him) in his interview, which was nice to see. But there were some key players left out of the story.
Also, I thought it was WAY too much Jakob Dylan. I'm from his generation, and I'm a fan of Beck and Fiona Apple and Regina Spektor, all of whom appeared. But the film purported to be a tribute to this 60s music, yet it kept cutting to Dylan's versions of these classic songs rather than the originals. Yes, I know, it was supposed to be a promo for Jakob's tribute album, blah, blah. Also, the interviews kept cutting to Jakob and his really useless, "Hmms" and "Yeahs." The way the interviews are shot, you see the subject and Jakob sitting next to each other, and it keeps cutting to him for his nothing reactions. The ending credits said "starring" Jakob Dylan" and featuring everyone else. It would have been nice for him to step aside a little bit, especially since he didn't have much to say.