Even if the word "choke" is used explicitly in the episode only by Rachel, this is actually a tale of three failures. And contrary to other episodes of Glee, where it can be fun to see some of the characters in trouble or where a bad thing is approached in a light, almost farcical, way, this episode leaves a strong bitter aftertaste.
The emotional focus is, of course, Beiste's story, one of the harshest themes ever touched by Glee. The rendering is especially effective because the authors wisely chose a pretty subdued approach (contrary, for example, to the bullying episodes). The way the girls' class was involved was not so clever and it didn't produce exciting musical results - I was not taken at all by the Cellblock tango, that I usually love, or by Shake it out - but the whole story arch and the bitter conclusion were very powerful.
Puck also has to deal with failure - his, and his dad's. Even if the storyline is a bit obvious, and even if a last-minute save is not really a great message (don't worry to study for the whole year, because at the end two words of a song will make you pass!), it is still a disappointment, especially because of the scene between Puck and his dad which was short but meaningful. I am a bit unhappy for this choice that means probably that Puck will come back for next year... Mark Salling really starts looking too old to play the high school kid!
The most clamorous failure is, of course, Rachel's. It is really cruel from the authors' part to make her fail the only really important audition in these three years! But I guess it's important to maintain some tension, considering that in this moment Glee has very few storylines really open. Speaking of which: why did Quinn disappear?
Globally, this was an episode focused on quite strong storylines more than on pretty weak musical numbers (I save only Kurt's audition and Rachel's Cry) - at least some minor characters had some singing! -, and provided strong emotions, in the best Glee tradition.