We aren't sure. But I personally think it has to do with passion. Even if you're amazing, and you don't show a passion, you won't get in. And if you do show a passion, but don't highlight it in your essays, you're screwed.
I think people place too much emphasis on SAT scores, for example.
One could have essays that just don't add to the application. At schools with admit rates as low as Stanford, you can't afford to not work that hard on your essays.
The other reason they made weird decisions is that they just can't accept everyone who is well qualified. With that many applications, chances are there will be some very strong applicants they just can't accept because there isn't room for them on campus. Everyone who is accepted has something great to offer the campus. There are some who are rejected who do too though.
Plus, sometimes people gloss over small reasons why people are chosen over others. People (and by that I mean applicants) are very number-conscious. It provides a means of comparison that allows one to be judged against another. It's evolutionary to compare yourself to others and go "that was a weird decision." Take me for instance. I had a 3.98 GPA and a 2240 SAT score. Nothing wonderful for Stanford. I guarantee you there were plenty of people with better numbers. But those numbers don't tell you that I have taken classes at a University since Eighth Grade. Or that I can name all 50 governors and practically have the C-SPAN schedule memorized. Or that I write very good and strong essays that build together. Numbers are easy to compare; people are not. Until you look beyond skin-deep comparisons, you will continue to think that some decisions are weird.
knightshield is absolutely correct. I totally agree with him.
"How do you know they received good recommendations? Did you read their recommendations that their teachers wrote for them? I'm curious, since I don't even know what my teachers wrote about me."
Perhaps the OP's counselor told him an example of a person who had this "wonderful recomendation" but unfortunately rejected from Stanford? My counselor did it. Perhaps the OP's counselor did the same hmm?
^Well one has to define what a good recommendation is right?
In my opinion a good rec is one that accurately portrays the student and shows both his strengths and his humanity at the same time. I'm sure that university admissions are all sick of lazy teachers or counselors that just tick excellent and give a bland essay about the student. My two teachers and my counselor all know me very very well and I was good friends with all three of them which I personally suspect helped me get into Stanford.
Also I agree kyledavid80 showing a passion is extremely crucial. I am crazy about chemistry and in my essays I made sure that that showed.
Im sure you can show interests OUTSIDE the areas of acedemic interests too?
Totally. My main essay for Stanford was me describing how it felt to walk onto the field for a marching band competition, conduct the band (I was Drum Major), and walk off the field. I said exactly what I was thinking, which I believe showed my passion for music as well as other aspects of my personality.
I think there's also a big difference in what an applicant sees when they look at their application, and what an admission's officer sees when they look at that same application. This is especially true when it comes to two things: EC's and recs. When it comes to EC's, I think many applicants think they need to have a certain amount of bredth, significant depth in a couple areas, and after that it comes down to winning the best award in whatever competition(s) you can get yourself into. I think that because practically every kid that applies to Stanford has all this stuff, they have to look deeper to try and see who they should let in; in essence, they can't just judge everyone on some arbitrary standard of merit, they have to see what kind of a person forms in their mind when they read an application. And believe me, they want to see a whole person, not just someone who won the biggest and best award. And so I think someone who is very accomplished can be put on the chopping block in favor of someone who gives a better picture of themself through their application.
As for recs, well, I think a lot of kids, through no fault of their own, get a teacher who thinks its their job just to write about how they got good grades, knew all the answers, and never fouled up in class. I actually don't remember who wrote my rec for Stanford, but I remember almost exactly meeting with one of my teachers to write a rec for my nomination for West Point. He asked me point blank what *I* wanted in there, and I told him everything. The good, the bad, the mundane - I wanted them to get the whole picture of me. I wanted them to see when and where I had struggled, how I handled the situation, and how I ultimately overcame it to succeed. Many kids who are applying for these top schools struggled only rarely in HS, admissions people know that they will struggle more in college, and I bet they'd rather have someone who knew how to overcome this inevitable intellectual road block, and perhaps had already dealt with it, than someone who was able to breeze on through without a care.