I enjoyed all the seasons of Genshiken, even the "Second Season" anime, as well as all the manga. Plus, I still have both volumes of KujiUn and the anime dvds as well.
I don't think people liked the progression of the story, how characters changed over time, but hey, that's school life, people graduate and move on, even if Madarame still hangs out in the club room.
I didn't find any of the characters unlikable, even if the fujos took over, at least they kept the club going, and still put out Maebetame. Hell, I could even deal with Kuchiki, which got good in the S2 manga when he was getting ready to graduate and got shitfaced drunk. I even like Nyako, but for some reason, my fav character is still from S2, as I just have a thing for "Rika"s.
Yeah, my taste sucks.