Perhaps the greatest gift of being human is that of rationality, the ability to see patterns in the world and to derive meaning from these insights. Yet there is also the danger of seeing things that simply are not present; patterns fraught with deep meanings to oneself that are simply not there in the world. So with the caveat that this is all just speculation (or madness), I'd like to provide a lame analogy as to what exactly happened in the Harpua, mainly piggy-backing off of what @JumpMang has already stated in the review section proper of the show.

Is humor meant to be consumed and immediately reacted to? Humor itself depends on the recognition of such patterns, as something unexpected that nicely acts as an outlier--showing us the patterns themselves. Stat geeks like myself are obsessed with Phish patterns (length of jams, quality of jams, bustouts, etc etc), and thus are obsessed with contextualizing a show to fit into certain categories that we use to consume the music. We carry this with us to every show. This is, paradoxically, categorizing a phenomenon (jams) whose entire spirit is meant to transcend categorical delimitations. It's a fine line between expectation and appreciation. Getting back to humor, the whole point is to show the absurdity of the human condition, the patterning, the expectations. We laugh because we are caught off guard, thinking we know what is coming, and of course realizing our error. That's the joke. Put like this, (though it is all good natured) ultimately every joke is on us.

Even humor itself has levels. Things that are lightly shocking put us into a place where we easily recognize the joke, and the butt of the joke is something we don't particularly hold sacred. Maybe some light conventional behavior that ultimately serves no purpose could work here, something we're not attached to. Yet humor can also strike home on a much more challenging level (think Kaufman, Lenny Bruce, or Carlin). Satire in particular is an enormously effective tool to use as a mirror to show us ourselves, our culture, our absurdities, our injustices. If one knows of oneself, one can ask the question--why? Is this the best way to be? Am I acting for a reason, using my mind to see better patterns, caring enough to change?

Alright, alright, I know this is quite the rant so I'll get to the point. Harpua has always been the ultimate in the 'what the fuck?' moments as far as Phish goes. Honestly ask yourself, WHY do people seek out the 'holy grail' of Harpua? I would hope it's about surrendering oneself to the absurdity of life and the freedom that entails, rather than simply because it is the ultimate Phish delicacy, the finest of rare Phish morsels. THIS particular Harpua I felt was of a much, much deeper level than the glorious surreality of Harpuas of yore.

I've got two points on the Second City bit of it. The first is that they are supposed to be terrible, that they are the 'straight man' portion of the set up that allows Mike to absolutely slay his narration with his impeccable timing and quirk. There are many instances of the banding acting themselves in a very 'what the fuck?' manner, if not downright making fun of the lameness of the whole bit. Second City people do some ridiculous, unfunny, and just plain weird bits and Phish (Trey, Mike, Fish at least, not sure about Page) rightfully take potshots at their nonsense. The Second City people were unexpected, but they weren't funny because they showed us nothing (in themselves) much less anything true about ourselves. On the surface, the comedy bits worked (see @JumpMang for the original point here) because they had both the straight (though still strange) routine and the wise-ass cracks by the band members.
It's like the tension and release in the jam--an almost musical back and forth that leads to the 'release' and funniness of the band itself, hilarious because of the tension invoked before. The Second City people let themselves be the butt of the joke.

Now the second part I'm probably reaching on, but I like where it goes so I'm just gonna say it. If the Second City people were that bad, made to be the butt of the joke, and generally had no other purpose on stage, then does this humor challenge us on a deeper level? It definitely caused some uncomfortable moments between a symbol of actual fans themselves (the Second City people) and the band. Could the Second City folks represent some darker part of ourselves that needs a cathartic exposing to the light of day? I certainly think so. The sign said "Poster Nutbag the RIGHT WAY." Think about what that means for a second. It was certainly a jarring moment when the 'fans' who were thoroughly clueless as to the chemistry of the band literally took over the stage and made the performance their own--relegating Phish to an afterthought. In every sense, the 'fans' had their own agenda and LITERALLY substituted their own narration for the bands'.

Truly deep humor can make us uncomfortable because it shows us things about ourselves that we perhaps are not entirely proud of. I think the Second City joke certainly showed me something about myself and my tendencies to judge the shit out of every single decision the band makes. Am I entirely clueless as to what the band wants to be--do I want them to be entirely what I want, entirely on my own terms? The simple answer is yes. Yes I do. And they are not that band that I want them to be, though they show frustrating glimpses of going where I want them to go. The irony of people judging the Harpua bit (deriding its length and the lack of jamming time) while entirely missing the point of the joke is just masterful. The subtly, depth, and freight-train-hitting-a-bullseye accuracy of this humor is starkly poignant and a thoroughly matured reaction to the band's aging and the fanbase.

The patterns we see are often obscured by the patterns we wish to see. To let go of them and enjoy life, sometimes we need reminders. I reserve my right to enjoy the jamming shows more than others, but I cannot pronounce the bands' intentions for them, or miss the excitement of something new, the new without which the band would die.