I think Eisenberg was a big issue as well. He's a good actor but was miscast as Atlas. I'm assuming this was his attempt at breaking type but I was never quite sold on it.
I thought Eisenberg was great in The Social Network and Zombieland but at the same time it's hard for me to imagine him playing anything (well) outside of those types of characters.
NYSM was OK to me. Wouldn't call it horrible. Yeah, there's some major suspension of disbelief. But everyone in my theater seemed to be enjoying it so I went along for the ride.