First caveat, it's been years since I read the novel. Second caveat, for the most part, I am a fan of Objectivism.
Atlas Shrugged was definitely a good read. I do have to admit, though, that the way Ayn Rand can occasionally use her characters just as mouthpieces is a bit obnoxious, and even to someone who buys into her philosophy, some of the chapters got tedious due to repetition ("This is John Galt Speaking", I'm looking at you).
I would also refer you to an interesting
essay, I discovered on the web. While I discovered it years after reading the novel, I think it articulates and pinpoints some reasons that explain and justify what had previously just been vague hunches, feelings, and musings as to why I preferred The Fountainhead over Atlas Shrugged.
Don't get me wrong, Atlas Shrugged is a nice piece of work, explores new philosophical territory, and is indeed thought provoking, but it could have easily done with some improvements as a literary work, in my opinion. I certainly would not recommend it as the starting point for anyone's venture into the works of Ayn Rand. That being said, if someone was of a libertarian bent, had already been exposed to and enjoyed Rand, and was looking for more, then by all means would I recommend it as follow-up.