Athrun pretty much had no choice but to rejoin ZAFT. The power and influence of the Seirans would likely have kept him from returning to Orb. The Earth Alliance would laugh themselves sick at the very idea. He was likely facing criminal charges from the PLANTS so trying to live there was out of the question. Rejoining ZAFT was pretty much the only option for him
Well no. He did have another option. Go with Kira and Lacus on the AA and be a third side again. And that's probably what would have happened had he curbed his unease and not immediately made for Plant. By the time he came back they'd already left and he was too wrapped up in Zaft when they appeared before him again. But if he'd stayed in Orb, then he'd have gotten the call the next day after the mansion attack for the Clyne Faction to regroup and he'd have done just that. It might have him, not Kira piloting the Freedom to interrupt the wedding.
True, had he stayed in Orb. But he didn't. Therefore, by the time he returns to Earth, Kira and the others are gone. Orb is firmly against him. This leaves him no choice but to then go on and join The Minerva, which leads to him becoming "wrapped up" in Zaft again. So he really didn't have any choice.
Despite claiming that he wants to heal the rift between Naturals and Coordinators, Durandal is clearly pro-Coordinator. His Destiny Plan is based on giving the best jobs for those with the best genetics. And Coordinators have specially modified genes. Therefore Coordinators would get the best jobs and use the money from these jobs to ensure their children would have the best genes.
Coordinators still have birth control and sterility issues that have not been solved. Durandal may seem like he's pro-Coordinator, but as a scientist he would recognize that Coordinators are not the next step in evolution like Patrick believed. It's probable that Coordinators would have stricter birth regulations because of these problems.
Another problem is the trouble people would go through just to sire desirable offspring. Arranged marriages would be the best case scenario- human trafficking for specific traits the worst. Going with the above of Coordinators having the most money, they could practically buy whatever mate they want.
The reason why Athrun and Cagalli's relationship wouldn't work out (according to Word of God, anyways) is because she's a princess, and he's an Ace Pilot. However, Athrun is also the son of a national ruler - the only reason he didn't take his father's place after Patrick Zala died was because ZAFT was not a monarchy.
The show implies that Athrun and Cagalli's responsibilities would pull them apart eventually, see the latter's arranged marriage. Even when that issue was resolved, there was still Durandal to deal with. Whether they'd stay apart after Destiny is anyone's guess, since we'll never get that movie.
On the surface, it seems immersion breaking that Kira was able to activate a reactor shutdown just before the Freedom was stabbed through by the Impulse. However, as soon as you remember the N-Jammers and that the Freedom needs to use an N-Jammer CANCELER to function, it makes sense. All he had to do was turn off the canceler and let the N-Jammers do their job.
There Are No Therapists seems unrealistic, especially in Shinn's case, but there are two points; first, a therapist can't help someone that doesn't want to be helped - you have to actually go to the appointment and put in what you can into getting better. Second, Durandal actively benefits from Shinn not getting therapy, and as he's ultimately his only superior officer past a certain point (and fully capable of over ruling any requests/orders to get him into therapy before that) he can avoid sending Shinn into it, all in the name of keeping The Brute on his team.
The reason Durandal wanted Shinn? Durandal already had his "Destiny Plan" system figured out before Kira and Shinn were born, or sometime later. Durandal analyzed Shin's DNA, probably a medical requirement for ZAFT, and learned he would be the perfect warrior for his cause.
Ironically, this would go on to be one of the primary factors in Durandal's own defeat: Shinn's worsening mental state did leave him an effective berserker, but it could only last so long before he'd break down entirely. And he does. In the final battle. Leaving him as nothing but a brute, too blinded by rage to even think about what he's doing, let alone actually use any tactics. And in particular, lashing out purely on instinct, which directly lead to Athrun curb-stomping him to protect Shinn's own ally.
One major reason for Destiny's problems is the What an Idiot! tendencies of the cast. Except...not really. First, compared to SEED which didn't reveal the Big Bad until later on, Destiny early on reveals who the Big Bad is. Second, no one in the cast knows this or has enough proof to do anything about it. Alternatively, they aren't in the right place to do something about anything or already are being manipulated quite thoroughly by said Big Bad. Third, aside from the majority of the cast being teenagers, the returning cast also has a lot of PTSD to deal with from the previous war. The idiot tendencies make more sense with a) some of the idiot stuff only seems that way to the audience who knows more and b) no one is very mentally sound due to the previous war and other contributing factors.
Cagalli's apparent Chickification makes sense in the context of her trying too hard to fill the big shoes her father left behind. She's trying to be a peacekeeper and Reasonable Authority Figure like her father before her. It's only after she gets a message left behind by her father that she decides to be Orb's ruler as herself.
If the EA's nuclear missiles weren't destroyed when they were, or the EA had built new ones, they could've been equipped on the Destroy during Stellar's sortie. Doesn't help that Stellar is also a crazy blonde, nor that Destroy's MA mode makes it look like a walking nuclear-equipped deathmobile.
On the subject of Stellar: she was never going to survive the series. Even if she escaped the Destroy with Shinn, she literally cannot survive without drug treatments that an Extended requires.
Fridge Logic and this — Think about the enormous affection Rey has for Gil. Now imagine every other "doctor" he encountered prior to Durandal and what he might have gone through, and (like Rosamia in Zeta) it starts making a chilling amount of sense.