One of the things I, as a mom of a current mid...love to do is attend local functions in our area that include both USNA and ROTC Officers. I have queried maybe 4 dozen in the past 3 years....always asking the SAME question..
Out in the fleet - is there a difference between USNA-trained Officers and ROTC Officers?
Without a doubt they all start with their beginnings. If the person went USNA they describe how much easier the transistion was from the Academy to Command and that their inner core of Officer-support throughout their careers remains intact. The USNA Officer can always count on invitations to USNA events and have that 'ole boy network' for socializing. Also USNA grads are overwhelmengly the ones with the longest time in service post-Commissioning, so if an Officer is looking at long-term career path, that USNA degree is a great asset.
If the person went ROTC they indicate how 'nerdy' the early adjustments of their USNA counterparts are, how the ROTC is better preparing their Officers for 'real world' interactions, how they learn to handle freedom at an earlier point in their college years, etc.
So the friendly rivalry is all part of any college-tension. Living in So.CA....the USC vs UCLA can produce equally firm positions, and it isn't even about the military!
But the ONE thing without question both sides agree on and this has been nearly unanimous:
In the first months of an Ensign's Career - the USNA grads are much more adept at fitting in and getting the command-position, job description etc. down. They are more used to living in that kind of environment. By 6 months out, however, there is virtually no difference in the caliber/quality/ability, etc. of any USNA young Officer. The Navy uses all kinds of schooling, education majors, experiences pre-graduation, personal history, etc. to make up it's fleet of Officers and they each bring to the table something that makes our US Navy the finest fleet in the world.
Now, in terms of the original question concerning your son: It is up to him if he wants to reapply to USNA. If there is any question in his mind, he should stay where he is. It is toooooo mentally tough on a person to have in the back of his mind: "geesh, I had it better in ROTC" when the going gets tough. Keep in mind the ROTC-turned USNA midshipman will repeat Plebe year. There are advantages in terms of military knowledge and you don't have the early classes, since your college experience is counted depending on the course and grade you received, but still you may have a young Second Class or First Class mid....barely older than you.....treating you like a lowly Plebe. You have to be mentally prepared to suck it up and deal with this. This may or may not be to your son's personal liking.
There are many mids at USNA with 1 year of ROTC under their belt. My mid is good friends with one young man, in her Class year, but 18 months older than her, who was rejected first round, went one year at a college in Wash. State, reapplied, and now is in his 3rd year at USNA. He'd be ready to graduate and be earning Officer pay soon had he stayed at ROTC. But he really really wanted a USNA experience. And so for him it was the right choice.
Now.....the other factor concerns Marines.....
They are an entire phenomenon all together and everything I just said throw out the window.
Every single Marine Officer, be they USNA, ROTC, OCS, has to experience The Basic School (TBS) where they are molded into the Marine mindset the MARINES WAY! And in my talking with Marines who came from all 3 ways to their 2/Lt Commission ------no one cares one whit about your prior education. It's what you do as a M A R I N E that matters, and that happens from second one of TBS down at Quantico. My girl will take this path and sometimes she actually whistfully looks at her Marine ROTC component friends who have already had many many trainings with the Marines while she is pretty much all Navy-scheduled for Summer training requirements that conflict with her Marine-heart. But that is the way it is for USNA interested Marines. And they too must suck it up until Service Selection, Commissioning and that trip down to Quantico.
Frankly whatever path your son chooses will prepare him well. May God guide his decisions.