I would say the most heavily emphasized topic on the MCAT currently, for which students are not adequately preparing themselves, is the molecular biology stuff. The AAMC has moved toward a lot more passages that involve pathways, regulatory molecules, cascades, etc. This is complicated by the fact that those passage types by nature are far more DENSE in terms of scientific language, AND they tend to use a lot of ACRONYMS, which increases the intimidation factor big time.
I also see a lot of immunology and bacteria/pathogen topics showing up at higher and higher rates on AAMC. This seems logical to me because they are moving steadily to all passages being based off of actual peer-reviewed journal articles. Those same types of things are heavy in the journals, so they are going to be more and more heavy on the MCAT.