The Fountainhead is a much better novel.
I did not like 'Atlas' since the characters lacked any depth.
The Fountainhead is a much better work on dealing with fighting for principles and not compromising with evil.
The Fountainhead was better as a novel. Most likely because the evils were personified and one could focus on them individually. Atlas Shrugged just has a bunch of interchangeable bureaucrats as the bad guys (accurate, but not dramatic.)