First and foremost, your nephew should do his best to have good grades since it matters to have those when he wants to become a pilot. The military makes it's decision based on the "whole person concept" so I suggest your nephew do ROTC, maintain a good GPA, be involved with the community, keep flying, be well-rounded and advise that he doesn't give them any reason for not selecting him when the time comes. I hope your nephew does well and gets to achieve his dreams.
And for those who are interested to know how it is to be in a military school, you may want to read this.