There are two central themes that surround most shows within the Gundam franchise. First is a constant but ultimately futile layer of anti-war sentiment. The second, and more iconic, is the Newtype. Other Gundam shows have come up with different terms for it like SEED, Innovator, and most recently, X-rounder. But their purpose as a form of biological evolution in humanity that heightens one's senses have remained the same. The franchise even built some of it's most iconic weapons systems (Biosensors, Psychoframes, Funnles/Bits/DRAGOON/Fangs) around a Newtype's mental powers. And last but not least, there's even a long running magazine named after this concept. This worship of the idea of the Newtype both within the franchise and on a more meta level is what makes one particular event in episode 3 of Gundam Unicorn so profound.
The OVA introduces new viewers to the concept of newtypes within the first episode. It was an ideal espoused by the founder of the Zeon Principlaity, of an evolution of man that could learn to communicate perfectly without misunderstanding. But the impatience of society as well as the realities of the geopolitical situation changed that term into ace pilots that altered the course of wars. Moblie Suite development had come to revolve around them in various ways and biological research attempted to produce Cyber (artificial) Newtypes. All of this to win wars.
But what if the military supremacy of a Newtype could be cast down? A Newtype's greatest weapon as previously stated was their heightened awareness of their surroundings and thus gained the ability to utilize remotely controlled turrets that fly about separate from the mobile suit and fire on the enemy from multiple directions. The system carried aboard the Unicorn Gundam was the NTD, Newtype Destory System. It uses the pilot as an organic processing device that converts enemy Newtype mental waves into hostility, and automatically activates upon detecting such hostility, not only giving the suite a dramatic increase in speed and mobility, but also the ability to essentially hijack an enemy's remote weapons.
All your funnels are...well, you know the rest.
The emergence of a technological countermeasure to a biological evolution marks the end of the latter. Current, the NTD system is difficult to reproduce, but as with all things, mass production is only a matter of time. What can a Newtype do when the battlefield tech reduces them to simply pilots with faster than usual reaction times yet again?
Now, I am well aware of the true end of the Universal Century time line, which Gundam Unicorn is merely a part of. The likes of Gundam F91, Crossbone Gundam, and Victory Gundam gives us a glimpse at events a century down the line where the above predictions do not actually unfold and the Newtype is still a battlefield center piece (especially in Victory). But the above gives us a glimpse of what is possible, and a potential willingness in the chronology of the franchise, not the Universal Century, to dethrone this long lasting being.
(I should note first this is only half of the thesis as it only addresses the military dominance of the Newtype. Analyzing the other side of the coin, the hero worship of this being across the franchise as the future of humanity requires a proper exploration of Gundam X, something someone else or me really should do eventually.)