G'day mate,
Well, since my $0.02 was asked for..
I know of guys and girls who've applied around about mid-way through Year 12, so perhaps if you were to put some work in between now and then and apply it may help you a little bit? Regardless, I doubt it'd be much of a worry if you were getting A's and B's (though I don't have first-hand experience to really comment). There are a few posters on the cadet forum who do stress grades a fair bit when talking to applicants about ADFA-entry aircrew specializations, though.
I share the same concerns as you do over my grades, as I'm not exactly an academic superstar. Personally, I don't believe being 16 will be a disadvantage to you as long as you come off as a mature personality -> I'd assume the psych would destroy the kind of bloke who says he wants to be a pilot because he'd "Get to shoot ****!"
