I made a list of what I need to know/do to in order to get into a PhD program and do well there.
Statement or Purpose
Letters of Recommendation (4)
Computer Science Background
Cognitive Science Background
The formal list is what they expect to see, as that is what they request. The informal list probably carries as much weight as the formal list, and possibly more. I need to have a solid background of everything listed in the informal list if I want to make up for the deficiencies that appear in my formal list. For instance, my math background is lacking; my last math class was nearly a decade ago, and my grade wasn't as high as I am capable of. My GPA, both overall and for my majors, is lower than what I am capable of. My transcripts show that I have incomplete and deferred grades for most of my graduate level research. I need to show that I have made up for all of that, that i am capable of completing the PhD program, and that I will do well in the PhD program.
My greatest weaknesses are my letters of recommendation, my research background, and my computer science background. Granted, I have both a BS and an MS in computer science. However, this did not deal much with the theory of computation, and other important topics. Also, I've been away from academia for a long time, and have much to relearn overall. The letters of recommendation will be the most difficult to get, as academics expect recommendations from other academics. My recent visit to my alma mater showed me that most of the faculty their either didn't remember me (understandable after three years) or were just ignoring me, due to not liking me or just being late for a class or meeting. I am unsure how to make up for this one. So far.