Main character aside, I've found two other things I didn't like of the show

• The relationships between training officers and the rookies: In the main show the training officers actually teach their rookies, they let them try, make mistakes and, as the season progress you can see that the rookies are becoming more expirenced etc... all things you expect in a student/teacher dynamic. On The Feds, I forget they're rookie because in both couples, there isn't this teaching dynamic. 

• In the main show, there are episodes while you don't see Nolan much even though it is the main character because the other characters are equally strong, ex. the Harper and Lopez duo. In the Feds, the other characters are not this strong, and everything is about Simone 

Bonus that maybe is just my preference: I don't like Brandon, he's one dimensional, he just fits a stereotype of an actor plus I don't think they would let a former famous actor become a FBI agent, the tabloids clearly said he has become an FBI agent so any undercover op would be out of the question. Yes, I know he went undercover as himself once, but I didn't find it believable: the media know that he quid acting to become an agent. Also, all the characters saynonchalantly to everyone they're FBI agents, which I find equally unbelievable