As a former AFROTC cadidiot i'll weigh in my 0.02. I've pretty much gone through both application processes, granted they were close to 5 years apart.
The Air Force:
Wonderful organization that takes care of their pilots, when and IF they become pilots. There are a ton of officer jobs that are not pilot, and a lot of those guys end up in fields that are as far away from aviation jobs as they can get (I know, counterintuitive, it is the Air Force after all). Whether or not those guys ended up liking their jobs or not, I'm not sure I don't talk to them as much anymore.
Yes the Air Force does give you a flight physical before showing up to OTS in Maxwell AL, but take it with a grain of salt. A buddy of mine got the flight physical, got selected for CSO (NFO equivalent in Navy), passed OTS with flying colors, then washed out at IFS in Colorado. He's doing alright now, but they are keeping him for the next 4-5 years and he's trying to get into the Space side of the Air Force. Air Force IFS has been known to have a bad reputation.
As far as my experience goes, did AFROTC for one year, but still disqualified vision-wise due to nearsightedness. Could have stayed in to fight the good fight towards pilot, but that would have involved A TON of paperwork as my plans were to take LASIK for them.
The Navy:
Not perfect, but also not bad so far. It's kind of a pain because I've been waiting some time to even know if I've been selected or not, but the experience with my OR (Officer Recruiter) has been very professional, up front, and honest: you really cannot beat that. All my paperwork was done in about 6 months spread out, and what I can take comfort in is knowing that the board WILL review my application and consider it, and ultimately give me a thumbs up or thumbs down.
Another buddy of mine did the NROTC route, he's flying right now. Still in the training pipeline so he doesn't have his wings yet, but nevertheless still flying. From what I've gathered the Navy will work with you if you want to become a pilot, but you have to work your tail off for it.
My motto lately has been Fly Navy, or Go Guard. PM me if you have any questions about either process. Good luck