I thought the Ferengi were a little two-dimensional. They weren't very convincing as villains, although some of the episodes they were a part of were interesting.
Fajo was a lot more three-dimensional, and if the writers/actors/directors had infused the Ferengi with the same qualities Fajo had, they really could have been "the bad guys" in a very unique way.
I don't think it helped that they decided to make the Ferengi look really ridiculous (I am sure many will disagree). They don't exactly inspire fear based on how they look, no matter what the storyline is.