NHK clearly tries to elicit emotional response from it's viewers - the drugs, hallucinations, suicide, the self-destruction, etc. are all meant to be edgy and pretty extreme at times.
Genshiken is just meant to make you laugh and relate a little to the otaku world. Genshiken is very light in its comedy and it's mostly meant to make you think "I could totally see that happening" or "That would be my reaction too" or "That's happened to me before." Probably the only solid emotional response I got from Genshiken was from Ogiue, who was such an adorable character.
The only solid things Genshiken and NHK have in common would be otakus. And amusingly enough Yamazaki, who was the original otaku of NHK, turned out the most normal guy in the show... just like Genshiken's crew was real down to earth.