If you think JACS typically publishes total syntheses, I really don't think you know what JACS publishes at all or you don't understand what's classified as total synthesis. JACS is a generalized, full-field journal. It publishes everything from structural biochem to catalysis to physical organic chemistry to materials science to synthesis. There is no unique emphasis on total synthesis. The unifying theme is that each work should contain results that are broadly applicable to the field and of interest to most of the readership (I don't know if you've ever seen the forms reviewers have to fill out but these are two criteria - the others are scientific validity and something else I don't remember off-hand). If you don't believe me, take a look at the current issue:
http://pubs.acs.org/toc/jacsat/current. Not a single total synthesis paper from my cursory glance.
If your friend got rejected from Phil Baran directly (who I presume was the associate editor assigned to the paper), then I presume there was something wrong with the work or it was a total synthesis that wasn't complete. Editors don't reject papers all that often before sending out for review unless there's something obviously or egregiously wrong with them. At least not for JACS.
I think it's outrageous for someone who worked in a lab for a few years at the bachelor's level to presume to understand academia. I spent years in this field thinking long and hard about how to secure a tenure-track faculty position. I did go to a good school for my PhD and I am most familiar with getting faculty positions at the top private as well as top public universities. I have a few colleagues who went to mid-tier schools for faculty positions as well. Perhaps your professors did not go through the current labor marketplace. It's insane compared to 5 or even 10 years ago. Too many PhDs are graduating. The top students from the top groups will go on to the top schools as faculty. The good-to-mediocre students from the top groups (who still have first-author pubs in good journals) trickle down to the state schools or go into industry. When a faculty position has 300-400 applicants, it can afford to choose the candidates that have been the most productive and have published in the best journals. That's the best indicator of the candidate's success as a PI. A job at my institution opened up last year and there were indeed 400 applicants for it. The search committee interviewed 20 applicants for the job and they all had impeccable credentials. I counted not one without at least a first-author
JACS pub. The one who was hired had multiple publications in
Nature/Science from their PhD as well as post-doc days. My colleagues at mid-tier institutions have similar experiences.
I know all this because I did give serious thought to applying to faculty positions before deciding on medical school. While I obviously wanted to end up at a top-tier school, I also looked a mid-tier schools. The implicit requirements are simply too stringent. Too many qualified applicants. You think medical school admissions is hard - try securing a tenure-track faculty position.