This is another one of those "clearly its not my Navy any more" threads.
In my day flight suits were organizational clothing, not uniforms. There was no such thing as "flight suit as uniform of the day". That was an Air Force thing, like the pretty scarves, and wearing your flight suit to work in the Pentagon.
If you were engaged in flight-related activity, you wore the appropriate flight-related organizational clothing, whether you were a Midshipman, an E-1, the CNO, or a movie star. When you were not engaged in flight-related activity, you wore the uniform of the day. On the other hand, if you weren't an aviator and not engaged in flight activity (like the Cruiser CO mentioned earlier in the thread) you didn't wear a flight suit just cause you thought it was cool. That guy, at one time, would have been very likely to get a call from the Base CO or TYCOM. The exception to that, late in my career, were SEALs who wore flight suits aboard ship, because the flight suit was actually the most suitable organizational clothing for the activities the SEALs were engaged in (lots of flying on helicopters and being around fire hazards). Also they thought it was cool too.
Some units (like the RAG) were tight about it and expected instructors to change out of their flight suits back into crisp khakis when they were done flying. Others (more common) were pretty flexible about aviators wearing flight suits during the duty day, on the grounds that you never really knew when you might need to go flying, to do an FCF or something. Nothing sucked worse than have maintenance call the ready room and ask "who's available to go flying" and miss out because you were wearing your khakis.
Middies on aviation cruises wore flight suits aboard ship for several appropriate reasons. One was morale/recruiting. The point of an aviation cruise is to orient the Midshipman to Naval Aviation, in order to attract those who would be capable and effective Naval Aviators. Another was that flying opportunities for middies were rare and you wouldn't want to miss out because you weren't prepared. "Waiting in the ready room for a possible flying opportunity" clearly qualified as flight-related activity, requiring the wear of the appropriate organizational clothing.
Regulating the wear of flight suits as a uniform of the day, while denying members of the Naval Service the opportunity to wear the organizational clothing appropriate to their duty (and apparently winking at SWOs wearing flight suits to look cool) seems like yet more examples of the Navy losing its way.