I chose ROTC over an academy. Here's my two cents, take it for what it's worth.
I knew I wanted to serve in the Navy since my sophomore year of high school. I have no military background or family history in any branch or at any school, so nothing of that nature was a factor in my decision.
When the time came to start college applications, I had a hard time deciding what route to take. I knew I wanted the regimented structure of academy life, but I was also cautious to accept something as binding as an appointment at the academy. I was fairly certain that the Navy was the career I wanted to pursue, but how could I be so sure when I had never really been exposed to it? What if I was stuck there for four years and in the service for another several after that and I hated it? It was an unlikely outcome, considering how dead-set I was on the Navy, but I decided that it would be a wiser option to pursue NROTC.
Now that I had made the difficult decision to rule out the academy, I had to begin looking at NROTC units. As mentioned earlier, I knew I wanted something structured like a service academy. This brought me to a decision between the senior military colleges, all which have a cadet corps and an overall atmosphere similar to an academy. I'm attending one now, have confirmed that the Navy is what I want to do, and am currently on scholarship and set to commission in a couple of years.
I don't regret my decision one bit. Even knowing what I know now, I would choose ROTC over a service academy. Academies provide a great education and are an excellent option for the right person, and I have no doubt that I would've been happy at one, but I've found that the diversity, freedom, and, most importantly, balance, ROTC provides has been a key component of my education and development as a future officer.
Instead of being surrounded by Navy all the time, I have a very wide spread of influences. I have friends on Army and Air Force scholarships in addition to my Navy/Marine friends, so I've become very well acquainted with the inner workings (at least on a ROTC level) of those branches. I have civilian friends pursuing everything from careers on Wall Street to careers in medicine. Outside of designated times for military training activities I'm free to be a normal college student at a great civilian university. I don't have to feel like I missed out on a regular college experience OR a regimented military lifestyle. And when it's all said and done, I'm putting on the same butter bars and going into the same service as any academy grad.
I can't say whether ROTC or an academy is better because there's no definitive answer. It all comes down to individual preference. I love my school and my ROTC unit and wouldn't trade it for an appointment, but someone else might want all-military all the time and hate the ROTC lifestyle. To contrast, I know several people who have done a year at my school and transferred to a service academy.
My advice to anyone trying to decide between ROTC and a service academy is to visit the schools they're considering and talk to people that attend them. This website is a great resource for finding people in different commissioning programs and at different schools. If there's any doubt in your mind about the military, remember: you can get out of a four year scholarship for free after your first year and stay at school, but getting out of a service academy will cause a huge hassle of applying to different schools, dealing with credits not transferring, etc. Consider a senior military college if ROTC is on your radar because they're a great balance between an academy and a normal ROTC unit. And, above all else, go with your gut. Only you can decide where you'll be most happy.