As far as I know, this was one of the reasons why the book was recieved negatively in Japan: People were upset that Naoto had no boyfriend in the book (either Yu or Kanji) which contradicted their headcanons from P4. This completely ignores, however, the fact that Naoto gets mails from Kanji and introduces him as an important friend of hers to the reader. There is also an image (drawn by Soejima) that shows Naoto holding hands with Sousei which caused a stir since it made Sousei look like Naoto's boyfriend.
From what I understand, Sousei was extremely disliked in Japan. The combination of him not really fitting in with the plot combined with what was perceived as extremely poor chemistry with Naoto didn't go over so well.
The translation that said that Sousei's purpose was to counter Aigis was based on the Persona Magazine world guidance thing that came out a few years ago and that translation seems to be wrong if you dig into the book. Sousei was simply meant as a back-up for Aigis and was ultimately deemed a failure since his Persona had no combat abilities. And while it certainly is an asspull, the part of the Kirijo Group that was responsible for Sousei's development was secret even within the company which explains why Ikutsuki doesn't know about him. Now, about that generation thing: Yuichiro Tanaka mentioned in the P4A interview that earlier generations had no human form, but Sousei was developed after Aigis.
Interesting. Where is this Yuichiro Tanaka interview at? I've read transcripts of the Tanaka interview from the Arena book where he mentioned that only the 5th generation onward were actual robots with personalities, but I don't recall it ever mentioning Sousei.