I took a course about a year and a half ago on Science & Technology policy, and we actually had a couple of lectures about publishing, academic funding, and the peer review process. Some of the issues that were discussed were the lack of an overarching guideline for reviewers, politics and cronyism, and the desire to publish articles that are "sexy" or easy to peddle. Do those sound about right?
Definitely a lack of guidelines. The rest as well. It's not all bad, but the process could be improved. Journals are almost unnecessary at this point, as they no longer serve their primary objectives as well as online services can. I don't read any journals. I peruse the literature by searching databases, and getting keyword-specific updates. The idea that journals have an impact factor creates bad incentives. It would be nice to lose that.