For the AFROTC it would be your CoC, but your FCC and CC will also have a voice in the decision making process.
I have to say IS is iffy for next yr. Right now they had enough for the class of 14, and if they are on target for 15 they may not offer any.
IS is always harder to get than the HS process, because cadets that didn't get HS will also apply for IS PLUS cadets who join as a C100 may also try. I think at our DS's det for his C100 yr, every cadet that was not on scholarship applied, probably about 30-40 cadets. Hence, it can be competitive.
You will need a strong gpa, better odds if you are tech. If you go on the AFROTC website there is a page on how to compete for one.
You also want a strong PFA score. The one thing cadets find out very quickly is that their scores change drastically, especially sit ups and pull ups, because instead of having a coach who will give you a pass on form, they won't. Practice that PFA properly and that includes the down time between categories. You can't go and do the run, and then 30 minutes later do the rest. That isn't how they will give the test. If it says X degree bent, than they mean X degree.
The PFA scores are about of your packet for every board. You want at least a 95-96. I would also suggest doing it O dark thirty, because that is when ROTC does it. Again you want to mimic the test to the best of your ability, don't do shortcuts, because it will bite you.
If they reopen the IS track for next yr. apply. There is only one certainty that any one can give you re:getting it. You have 0% chance if you don't apply.
Good luck.
Side note for 16 candidates who are applying for the AFA, apply for the ROTC scholarship. I can't believe the numbers of AFA candidates this yr that stated they did not do plan B. Next yrs AFA is suppose to be as competitive as this yr., probably even more so due to the economy. Don't miss that opportunity.