My take nowadays (I was 15-16 when Pepper came out) is that there is a loose concept, "We're not the Beatles. What you think the Beatles are is not who we are--we finished that on Revolver." I think it's a good album, but not a strictly cohesive one. Along similar lines, "Face to Face" by the Kinks develops several themes (especially appearance vs. reality, and memory vs. experience), and artistically / thematically speaking is (for my taste) a better work of art. "Freak Out" (which you mention) is similar--not cohesive but unified by the artist's vision.