Our high school has selective admission and allows to skip a grade upon admission. This is why approximately a half of our graduating class is 16 or just turned 17 by the time of graduation. Our college counselor says that these kids are at disadvantage at top tier schools (and we are talking about just 1 year, not 3!). According to her information, these schools think that younger kids are not mature enough to live and study independently. Moreover, Ivy League admission is almost like a lottery now, so it will be very unwise if you'll choose only from them,their decision may hit your son pretty hard. Backup plan is a must!
So, my advices will be:
1. Ask your college counselor to e-mail the top universities of your choice about your situation, their attitude may vary from school to school.
2. Choose wisely, state universities may be more forgiving, and at the big university your son, being as smart as he is, will always find intellectual peers, there is a lot of smart kids at state schools.
3. Sincerely, I do not think that you can change something for the application to become more attractive for the top schools. Your son definitely bought his lottery ticket, but his age may serve either as a huge disadvantage or as something that catches attention of an admission officer. You will never know, they reject you without explanations.
