Having straight A's in all of your subjects is not everything that you need. Heck, I can easily list out a lot people in different schools having the same academic capabilities. Universities like MIT, Harvard, Yales, or Stanford get a lot of applicants every year, and I'm sure that most of them have really good grades.
My point is, they (universities listed above) look for people with special & rare capabilities (someone that believes in change) which are shown to them from your non-academic activities. Apart from that, your essay plays a very strong role that reflects your thoughts and aim; your interview of course will somewhat let them know a little bit about your personality.
On the other hand, having strong leader-ship skills is not everything either. You are special and different from everyone else so you have to show that to them. If you deserve to get into Yales then you will, if you get deferred then apply again.
Just be confident! and your grades are really good.