First thing to know is; you have a 100% guaranteed chance of NOT receiving an appointment to the academy if you don't apply. So always apply. No, it doesn't look bad on an applicant who applies more than once. Matter of fact; the academy board, who are humans, actually see repeat applicants as committed and determined. That's a good thing.
Next; who's to say your brother's grades are "Marginally" qualified. That's like being marginally pregnant. You are...... or you're not. In your brother's case, 3.6 gpa is qualified. As for "Marginally", that's totally dependent on who is "Competition" is. In other words, your brother could have a 3.9 gpa and still not get in, because all those he's competing against could have better grades.
But simply saying his GPA is a 3.6, is totally misleading. A 3.6 gpa in all AP or IB classes will beat out a 3.85-3.90 gpa if it's in just state minimum required classes. Also; while academics makes up for 55% of an individual's application score, the GPA is only a percentage of that 55%. If your brother nailed 30+ on his ACT or 2100+ (3 tests) on his SAT, that would mean more and bring that academic score up tremendously. Same with class ranking, difficulty of classes, etc... But even with all that said, academics is only 55% of the total score. 25% of the score is based on extracurricular activities, athletics, leadership, community service, work, etc... If he's a 3 sport varsity starting player; captain of team, class officer, leader in a club, volunteering hundreds of hours to the community, etc... then that 25% can get him a much higher score too. Same with the remaining 20%. That's where admission liaison officers like me or Flieger's opinions and interview count. Where your application/writing sample/teacher's recommendations, etc... all come into play. ALL of these scores together is what gives you a final composite score. And it's that final score that matters. Not just a gpa. So definitely have him apply.
And remember: There isn't some magic list with check boxes that if you do all these things, you receive an appointment. There will be approximately 6,000 individuals who will have all these things mentioned. Of those, approximately 2500-3000 will completely qualified medically, academically, and physically. And of those, only approximately 1000-1200 will actually receive an appointment. What that means is, it depends WHO in your congressional district; who in your state; and possibly who nationally; you have to compete against. I.e. a 3.6 gpa, 29ACT, 2 sport varsity athlete, boy scout, etc... applicant in one state might receive an appointment...... while a 3.85 gpa, 32ACT, class president, JrROTC, etc.... in another state WON'T receive an appointment. That's because they are competing against different applicants. And even the 4.0 gpa, star athlete, 36ACT, etc... if they don't get a nomination from their senator, or representative, or from some place else, WON'T receive an appointment.
In a nutshell.... the application process is too in-depth and too complicated to ask if a person should apply based on a gpa. Yes, you apply. If the gpa is TOO LOW; e.g. 2.1gpa, you'll be told you don't qualify. But a 4.0gpa with a 24ACT ALSO DOESN'T QUALIFY because the ACT score is too low. It's a total package. Not just a gpa. Have him apply. That's the only right answer. That's the only way you have a chance. And you will never be looked down upon for applying more than once. Best of luck.