I care a little about your GRE scores, it is a filter, you need some kind of standardized comparable. Congrats on getting in the 99th percentile (that's expected). I don't care much about your GPA. I might look at what classes you took. I will probably look at your reference letters briefly. They might be from professors, they might not. I don't care. I love the fact that you have some startup or industry experience, you are slightly more likely to actually know how to get things done.
The very first thing I read is your cover letter, then straight to your research statement which I will read in great detail. The only thing I care about is do you have a passion for research, are you likely to be successful at it.
At most research institutions in most areas of science, we have to pay our graduate students stipend and tuition, either right away or after a year. This is a damn good incentive to get students in who are going to do great research.
All I care about is getting great researchers in the door and (eventually, hopefully) into my lab. So, my advice: focus on your research statement. Tailor it to the department your are applying to, talk about the research they are doing there. But, have your own agenda. At least know what research areas you are passionate about.
The GRE point I was trying to make was that since 99th percentiles are expected, the test shouldn't exist at all as it is clearly a poor filter.
Honestly, I think you dodged a bullet. Academia isn't that magical (CS PhD here). I think you get a better education reading Hacker News some days.
Now on to the game of academia. It is one that is based on reputation, papers, and not money. No one cares for efficiency either and no one is building crap. All they are doing is trying out different "solutions," which may or may not make any sense. For instance, "hey guys, let's apply game theory to problem X, it will be a good/novel experiment and we can get a paper out of it." Waste of tax dollars. The logical answer that solves problem X might have already been solved and can be solved using ordinary methods, but academia doesn't want that. Research labs have business models, keep proposing new complexity on complexities, very unnecessary. Overcrowded fields like computer vision reek of this.
185 dollar GRE that I can get in the 99th percentile on with ZERO studying? Grades that aren't normalized across institutions weighed heavily? Need recs from established professors who can slip in a good word for you?
Oh sorry, you were actually doing things that interested you, not necessarily things that would impress the right people. Oh sorry you took tons of hard classes at a prestigious institution and so have something less than 4.0. Oh sorry you hopped labs for a bit instead of staying with that boring CS guy that would've gotten you into any PhD program in America for 4 years. Oh sorry you spent a year or two out of college doing startup tech work without building credentials with other PhD grads but nevertheless solving research grade problems.
I've realized that the PhD admissions does not select candidates who actually want to do research. It selects candidates who want to be admitted into a PhD program. No thanks. I love science and math, and I love research, but I think the PhD application has been so harrowing for me, I won't consider it again unless drastic changes are made.