Speaking from anecdote, there is a difference between the Naval Academy
officer and the NROTC
The NROTC officer is ordered to abandon ship, does so, and immediately drowns.
The Naval Academy officer abandons ship by performing a dive from a 10 meter platform, hits the water without sustaining injury, then swims underwater for at least 30 meters in full khaki uniform. Upon completion of the 10 meter dive and 30 meter underwater swim, he then performs a full trouser inflation and awaits rescue. When no rescue comes, he decides to swim for the coast. He successfully swims for 40 minutes demonstrating at least four different strokes with proper form while still wearing his uniform. At this point he then drowns.
All joking aside, there is little difference between an ROTC officer and an Academy officer. Originally, the Academy was intended to be the professional school of the "career" officers and a far more difficult road to travel, while the ROTC program would produce the "five and dive" short term officers. That simply is not the case anymore. My sponsor father is a P-3 Orion pilot, and an ROTC graduate from UCLA, having just finished up on 20 years.
There's really not much of a "quality of officer" issue anymore either. The best commanding officer I've had to date was an ROTC graduate from Florida. The current Commandant of Midshipmen is a Marine Corps colonel who graduated from the Naval Academy. He is not only erudite, but the kind of guy who would lead us into the valley of the shadow of death, and we would fear no evil because he is the baddest mother in the valley (TM). The deciding factor in the quality of an officer is the officer's desire to perform at their best, not the ring they wear on their finger or the diploma on their wall.
My personal opinion is that we have both the ROTC and the Academy because the American public respects and values both. The nation looks at ROTC as a way for average young adults to earn an education and serve their country. Meanwhile the Academies are an institution representing the values and morality of the nation. When the public ceases to will either into existence, it will cease to exist. It's that simple. Much like General Kelley said of the Marine Corps: "It exists because the Americans want it to". I think that while Academy grads always look at ROTC grads in a different light (mainly because the ROTC experience is intended to be different than the Academy experience), the mutual respect far outweighs the cliques that outsiders might believe would form.