I went through the 4 year AFROTC program. The school that I attended did not offer AFROTC, so I went to Loyola Marymount University for AFROTC (AFROTC no longers exists at LMU). Cadets like myself were referred to as "cross towners". If I had to do it over again, I would opt for the 2 year program (if it still exists) since you only have to march around for 2 years versus 4. In all seriousness, if you are serious about becoming an officer, the 2 year program is the way to go. If you are not, then try out the first 2 years without any obligation and then you can decide. The last two years is when you sign on the dotted line and choose what you would like to do in the AF.
Now, if you are looking for a scholarship, the 4 year plan is a better deal. I've been out of it for a while so I would check with the ROTC detachment at any of the schools that offer ROTC.
As for flying (AF vs. Navy......), the needs of the "service" come first. I can only speak for the AF, but I think you would have the best chance of flying your choice of aircraft in the AF, as long as you finish high enough in pilot training. Like Dragon said, you could be the top guy/gal in your class and still end up getting something you didn't want, all because of the "needs of the Navy/Marines, etc." From my experience, if you do well enough in UPT, majority of the people get what they want.
The service academies are outstanding, but I would seriously consider how much you value your freedom and social life. That's a whole different can of warms! Anyhow.... good luck!