I believe it is the Aeon ending Because:
The Aeon ending is the true one, because the Black Sun was indeed fired, even though Burke stood in the way of the beam. The energy of the beam was necessary for the Seraphim to cross the galaxy, and even though Burke intervened and no planets were destroyed by the beam, the Black Sun was "FIRED" (thats the important) towards Burke and it was destroyed. We see this in the final mission of Forged Alliance, in the following dialogue:
Fletcher wants to fire the Black Sun out of paranoia, saying "You sold us out Hall. Allied us with monsters and freaks. Once I get my hands on the Black Sun, I'll be able to REBUILT it and end this once and for all."
To which Hall responds, "What the hell are you talking about? The Black Sun is DESTROYED. The Aeon and Cybran are our allies.
So yes, the Aeon ending is the true one, but anyone who says that Burke's consciousness merged with all of humanity after receiving the blow of the beam is mistaken. The reality is that after she was struck by the Black Sun's beam, she became one with the quantum realm (There is no exact definition for what this means, but she mentions that now her vision is perfectly clear, nothing scapes her sight, ), but her consciousness was not transmitted to all creatures. Therefore, the alliance between all factions is achieved.
- "Black Suns make me one with the quantum realm. For the first time, my vision is perfectly clear, I see everything, nothing escapes my sight" (at the beginning of the Supreme Commander campaign, we can see her saying that something obstructs her vision, so she achieved a step towards something greater).
- "I am truly one with the Way" (she became one with her doctrine, she embodied the doctrine itself, she did not expand her consciousness to all creatures, but rather, she embodied the doctrine as a "God").
- "Humanity (only humanity, not the Seraphim) has been pulled back from the edge. The future is free from war, conflict, and tyranny.
- My path now lies elsewhere. I must explore what I have become" (she still doesn't understand what she has become and the extent and repercussions of this).
- "You are my champion, you will care for those I leave behind."
This is the true ending, a peace between factions, between humans. All three factions, Cybran, UEF, and Aeon, are humans. Aeon are humans taken from the Seraphim to show them the "Way", . Cybran are also humans with mechanical parts, but they are humans. Now that there is peace between them and "no war between them," they must fight an external threat. THIS IS WHY THIS IS THE TRUE ENDING.
Remember that the seraphym were recruiting species from around the galaxy to show them the way and cleanse the universe of all species that opposed them, just like Marxon did. And the Aeon are the individuals of the human species recruited by the Seraphym. But Princess Burke had another "path" another "inspiration" she reached a step further in enlightenment, she preached a different doctrine than the one the Seraphym taught them, a different one than the one Marxon preached.
Cybran ending: Quantum Gates still works, so Cybran ending cant be.
UEF ending: Balck Sun were not destroyed, and core planets werent destroyed by black sun beam, so UEF ending cant be.
BONUS: i recomend you to read the princess Burke dialogue at the end of Supreme Commander 1 campaign, it is sublime. About the symbols, ther meaning, and the freedom.