[Klashikari]

I'm not sure if the "plot" is the problem here, because considering how went the stalker points prior the first BD results, that trend was already present for quite a while, even before we got the "disappointing episodes".

I believe a lot of circumstances went against Chu2koi Ren

1) Due to its chuuni comedy nature, its "fresh" impression was lost de facto, so of course it will attract far less curious buyers.

2) Due to being a sequel, it is obvious it will not sell as much as the first season (there are VERY few exceptions to this rule, generally very big franchises)

3) Chu2koi S1 was aired on Fall 2012. Chu2koi Ren aired on Winter 2013-2014. What does it imply? Timing of the BD. Chu2koi Ren vol1 is being released during a very very busy time of the year: end of the second semester for high schoolers, exam entrance preparations, many events being scheduled, video games releases etc.
So you have free time and, sometimes, budget being quite limited. Even other big contendants like Mikakunin and Saki barely made to the 5-6K treshold. Only Shingeki final BD could break 10K benchmark, so it tells you a lot how march 2014 was harsh on people more than usual.
So unless you have huge blockbuster like Madoka, Nisemono or LoveLive, sales for winter series are pretty weak in general.

4) Unless I'm mistaken, the first BD of Chu2koi Ren doesn't have any event ticket or record about the seiyuu, unlike the first one that had the latter. This is important since Chu2koi seiyuu weren't exactly known back in S1, so people were way more curious about them, especially Uchida and Sumipe.