The Letters section of the January 2007 issue of Physics Today (page 10) contained a discussion about the exacting and often confusing electronic paper submission process as an obstacle to getting published. I think a much more important and corrosive impediment to publication is single-blind peer review.
Peer review is the cornerstone of scientific research and advancement. It recognizes the importance of the objective reality and is a manifestation of the scientific method. It also keeps crackpots and just plain bad science out of the journals.
However, the single-blind peer review system has a fundamental flaw. It allows reviewers to assess the author(s) of a paper along with the scientific content and thereby permits nonscientific considerations to creep in. As is often true in other aspects of professional life, in peer review who you know can be as important as what you know.
Single-blind peer review discourages scientists from publishing in new fields, suppresses research from unknown or unaffiliated scientists, and adds irrelevant considerations to the review of scientific content. It may, in fact, be robbing science of its greatest breakthroughs right now. More than 100 years after Einstein's miracle year, what are the chances that an unknown 24-year-old patent clerk could revolutionize physical law in a peer-reviewed journal today? It seems extremely unlikely.
The arXiv.org server suffers the same problem in that an author must have a personal reference in order to publish; in fact, there the personal relationship is paramount and is presumed to subsume scientific merit.
If journals are really about scientific truth and integrity, and if we believe in the objective reality, peer review must be double blind. The single-blind system is intellectual laziness at best, cronyism at worst.