Gundam SEED, Kira nearly losing himself to becoming a ruthless killer and was willing to kill his best friend while in the Strike Gundam, now picture Kira giving up his pacifist ideals in the Freedom...Old King would be proud, and given the extremely Crapsack World that SEED presented itself in, Kira was a Nightmare Retardant for what is a dark entry into AU gundam.
In Mobile Suit Gundam SEED Destiny the crew of the Minerva discover a hidden facility of Blue Cosmos where they condition children to artificial coordinators, how long do you think it was abandoned, a few days, weeks, or months? How about the children who were in them, where they still alive or dead for how long? And how about the method they used to make them into artificial coordinators seeing how they tend to get excruciating headaches, and freak out, what methods did they use which result to that?
The ending of Mobile Suit Gundam SEED Destiny has Cagalli resuming control of Orb, becoming one of, if not the de-facto, leader of earth. Meanwhile, Lacus has become ruler of the PLAN Ts. While this is all well and good, this means that if Kira and Lacus marry, and with them it seems the question isn't "if" , that would put the whole Earth Sphere under the control of a single family. Not only have we seen in the past where that could go, but there's the fact that if it were revealed the Cagalli isn't the biological daughter the Orb royal family and is Kira's twin sister the whole thing would fall apart. Our heroes have to lie to the whole of humanity for the rest of their lives.
Third Generation Coordinators are having a drop in population due to reproduction organs failing. This emans nothing to Kira, who is a first generation perfect coordinator... But the same can't be said about most of the other main coordinator cast; such as Lacus, Athrun, etc...