Without Kira, Lacus doesn't have a traumatized man to settle down with, so she might not retire with the Archangel crew on Earth. She might remain a prominent figure in ORB. Which means Durandal can't replace her with his own puppet. Which means that Durandal has less public support. Durandal may not be able to retain territory on earth when ZAFT begins "liberating" territories from the Earth Union. Durandal might not be able to push his plan at the end of S2 at all, unless he assassinates Lacus and his other enemies, but that's just begging for a civil war to happen inside the PLANTs.
I'm wondering if the Clyne Faction within the PLANT Supreme Council might be forced to relocate to Orb if Durandal tries to purge the SC of those who might not support the Destiny Plan. Alternatively, you could still have Lacus remain a prominent figure within the political circles of the PLANTs, though her role as the ceremonial leader of the Clyne Faction means that Durandal might have a harder time trying to get into power. It would be basically Eileen Canaver having a longer reign in the PLANTs, theoretically giving her more time to fix the damage that Patrick Zala had inflicted on the PLANTs. In this case however, the Atlantic Federation might actually annex South America, since South America was aligned with ZAFT in the First Bloody Valentine War.
The absence of Kira also changes what happens at ORB when Athrun comes back from the PLANTs. Cagalli is still there and hasn't been kidnapped by Kira. Cagalli was portrayed as a very weak willed person in Destiny, so who knows if she would just accept being married off to Yuna despite being engaged to Athrun. Assuming she rejects Yuna and marries Athrun, then Athrun has something tangible grounding him to ORB, and might not go back to the Minerva and ZAFT. With the announcement of the princess of ORB's marriage to Athrun, the Archangel crew would probably join ORB. ORB then reveals the Akatsuki that Cagalli's father had left behind for her. A coordinator from ORB's military could be found to pilot it, mentored by Athrun.
I would suspect that Canard Pars (the guy from the SEED side stories) might become the perfect fit for the Akatsuki, though I'm not sure where he and Prayer Reverie would be located in this scenario.
It might also be a political suicide within ORB if Cagalli doesn't go through with the unpopular marriage to Yuna Roma Seiran, though I'm not sure if the Drop the Ruins of Junius Seven would still occur at this point. Although would Durandal be willing to risk whatever political capital he has in engineering such an incident that would lead to the Second Bloody Valentine War?
With the hero of ZAFT having married into one of the most powerful countries on Earth (and the only Earth country notable for having Naturals and Coordinators), and with Lacus remaining a powerful figure in the PLANTs (and endorsing Cagalli's and Athrun's marriage), relations between the Earth Union, ORB, and the PLANTs would probably begin to normalize. The heroes would have much, much more public support than they did in canon, as well as much more in the way of strategic resources. It would be very difficult for Durandal to enact his Destiny Plan through force like he did at the end of Destiny, and if he did he would lose like in canon. After the defeat of Blue Cosmos, his term as president would likely be peaceful. He might try nudging the world towards the Destiny Plan through subtle legislation, but nothing would happen during the immediate years.
I would suspect that Durandal would try to lay low and create a power base of his own to gather like minded followers who might agree with his plan. However, with his background as a scientist, Durandal would still be pressured to find a solution to the infertility issue facing the third generation Coordinators.
While I agree that there would have been a significant improvement of relations between the three sides, there's still Blue Cosmos and LOGOS to contend as well. It might be a lot harder for Blue Cosmos to get involved in the second conflict while relations are improving.
Did Kira publicly known as the pilot of the Freedom Gundam, and a hero was instrumental in the first war? IIRC Shinn only started targeting Kira once he saw the Freedom return half way through S2, and then found out who was piloting it. Shinn would join ZAFT anyway, as he viewed ORB as weak.
If ORB assists in fighting against Blue Cosmos, then Athrun would likely kill Stella, which could lead to Shinn fixating on King Athrun as the target of his revenge (on the other hand, Shinn's resentment of Athrun built up over time, whereas here Shinn hasn't seen Athrun since episode 8, so he might let it go). This could complicate relations between ORB and ZAFT which Durandal might exploit, but again the heroes are in a better position than in canon, so the outcome would likely be the same.
I'm not sure if the Earth Alliance would be open to the fact that one of their own aces is a Coordinator (despite the Eurasian Fed having their own ace in Canard Pars), which might leave them open to criticism from Blue Cosmos (Kira would have been a significant target for Blue Cosmos in this case, even before joining the Earth Alliance). Alternatively, ZAFT wouldn't want to admit that the thief responsible for stealing the Freedom Gundam is a coordinator fighting against his own people as well.
On the other hand, Shinn being with ZAFT this time around might be complicated by the fact that the ZAFT leadership would not turn a blind eye to his behaviors and other antics. The only reason why he was able to get away with a lot of things that would have landed a regular grunt in a huge heap of trouble was because of his status as a war hero and an ace, plus being a double recipient of the Order of Nebula and a status as a member of FAITH. In this case, most of his misconduct would probably be seen with a massive critical eye by the likes of Talia Gladys. Moreover, would ZAFT actually be willing to induct someone who was psychologically traumatized in the last conflict? That trauma alone was the focus point of his misconduct.
And I doubt that Shinn would have met Stella in this scenario, mainly because the incident at Armory One would have played out a lot differently.
