There are several problems with the secret government aircraft hypothesis.
1. When the phenomenon first appeared, top Air Force officials had no idea what it was. This was their stance publicly and privately. Many classified documents that have come out clearly show this was the case.
2. The Air Force asked the FBI early on to help investigate and identify the sightings. If these were secret aircraft the Air Force wanted to keep under wraps, why would they involve other agencies? Indeed, the FBI heard rumors from individuals speculating on whether they could be secret air craft. They expressed a desire to make sure this was not the case before they undertook any investigation as they perceived that it would be a waste to expend resources trying to identify something that was already known. The FBI was subsequently assured by George Shulgen, then commander of the AAF, that he was unaware of any Air Force projects matching the descriptions and characteristics of the sightings. None of this is conjecture. It is all part of the historical record. If anyone doubts my account of it, do the research and examine the paper trail for yourself.
3. Many sightings have occurred over residential neighborhoods, densely populated urban areas and events where thousands of people are gathered. These are not the areas one would test fly secret aircraft in. Military testing of classified, secret aircraft has always been done in seclusion. Any intelligent military commander would not put the most secret aircraft he had out in plain sight for all to see.
4. Many of the maneuvers observed by these objects would quite simply kill any human pilot. The only way they would not is if we had made some kind of huge breakthroughs in physics, aerodynamics of aircraft, inertia, antigravity propulsion, etc. Whether we have any of these capabilities today is debatable. However virtually all UFO historians and researchers agree that there is no way we could have had these in the 1940s where these objects exhibited the same characteristics they do today. (We didn't even have supersonic flight in the 40s).
5. There have been countless dozens of military and government officials who have come forward saying that even at the highest levels of government and the armed forces the origin of this phenomenon remained a mystery. A great many have provided convincing evidence of this. Conversely, there have been precious few who have come forward saying anything to the effect that these objects were secret military aircraft and none have provided any evidence to this effect.
6. The test flying of experimental aircraft is carried out on a very limited basis. The very idea of "experimental" means that there are a limited number in existence, performing tests of varying degrees. This is not the case with UFO sightings. There have been tens of thousands of reports of all kinds of objects flying in all parts of the world. If these aircraft have a military origin, they are part of a program that is fully operational and functioning across a very wide spectrum. These vehicles would already have been mass produced and would now be part of an extremely large military arsenal. Such a program, no matter how well guarded, would be impossible to conceal from the public. This is especially obvious when you consider the global nature of the UFO phenomenon. Many sightings and reports come from remote corners of the world far from any US military bases or lines of supply. All currently operational military aircraft are well known, even covert application craft like the stealth fighter and bomber. Why is this? It's because such a secret could not be kept even if it was desired. Too many people have to know. Military officers, air intelligence analysts, mechanics, civilian contractors of parts, politicians, accountants, news media covering military operations, etc.
The notion that all (or even a great number) of UFO sightings represent secret military aircraft clearly ignores these unmistakable problems.