Cliché Storm: Lacking any deconstructive aspects that separated the characters from the standard personality types they were based off of, you're left with a fairly average paint-by-the-numbers shoujo romance.
Just Here for Godzilla: If you’re not interested in romance then the mythology gags are plentiful and a number of fans just came because it was the first Haruhi anime related content released since Disappearance came out in 2010.
In Chapter 10, Ryoko starts revealing embarrassing secrets about Yuki to Tsuruya, who does the same with Mikuru. Tsuruya then reveals that Mikuru has a star-shaped mole on her chest, which is something that Mikuru did not know before and is greatly embarrassed. Now, in Ryoko's case about catching Yuki checking her weight after a shower makes sense, since she's a close friend who frequently visits her, but, for Tsuruya to be the one to know about Mikuru's beauty mark is, while funny, a little strange, since it's not really explained how she knows...Not to mention that Mikuru looks seductive in that page.
When discussing Valentine's Day, Mikuru says she would be happy to get chocolate from Yuki if Yuki were male, and sheepishly admits that it came out like a confession.
TAAKII! became one on /a/ after the very first episode of the anime.
The return of a single phrase that reopened some old wounds and made many a viewer cringe (shortly before laughing their asses off): "Kyon-kun denwa!"
They Wasted a Perfectly Good Character: Taniguchi and Kunikida, Kyon's existing friends before meeting Haruhi. The two were extremely underutilized in the original Haruhi Suzumiya, playing only minor roles at best despite having defined personalities. Given the premises' focus on the relationship between Kyon and Yuki, one would think this would've given the writers the chance to give them some screentime and focus without Kyon's social time being dedicated to the SOS Brigade. But as early as Book 2/Episode 3 Haruhi is introduced into the story, bringing Mikuru and Koizumi (and a cavalcade of nostalgia objects) with her and reforming what is effectively the SOS Brigade again. The series decided to focus on this timeline's SOS Brigade instead, thus repeating the same lack of use as the main timeline.
Alternative Title(s):The Vanishing Of Nagato Yuki Chan