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.
Well theoretically he could have just taken his fancy new flying Gundam ignored Durandal's orders and flew around looking for Archangel to join up with them. Or assuming he doesn't want to steal yet another Zaft Gundam and get them even more pissed at him, simply politely decline Durandal's offer and request a flight back to Earth (Durandal likely wouldn't arrest him if he refused given that he's pretending to be a nice guy and he could have just made that open threat from the start) and then go find them using conventional transport. It would take a good while but Milly eventually met up with them so it's not impossible. This would however basically remove him from the show for a good long while.
However, all of this and the below supposed failure of their relationship presupposes is based on the fact that Athrun HAD to leave in the first place. Thing is, he didn't have to and wasn't gonna. Until he found out that the culprits for the Break the World incident were his father's fanatic loyalists, it didn't seem like he was gonna leave Cagalli's side. Learning who they were flared his old unresolved sense of responsibility to his homeland, causing him to relapse and effectively leave Cagalli, unwittingly to the wolves that are the Seirans. This, in turn, causes Cagalli to lose her last immediately available emotional support and break at cascading speed, with only Kira saving her from the terrible fate and ultimate indignity of being Yuna's trophy. It's hard to say how much Athrun caused this, but his abandonment of Cagalli just so he could act on his feelings of loyalty to his homeland (and be completely ineffective about it in the end) definitely wasn't an insignificant factor.
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.
Furthermore, his survival. The writers had to do it like that, in order for not just Kira to survive, but SHINN as well. Look how trashed the Impulse was from the explosion of the Archangel's decoy. Imagine if the Freedom did explode in a nuclear manner. Given what we've seen of nuclear-powered suits exploding in other shows, and the non-nuclear-powered Aegis self-destructing while clamped onto the Strike, the Impulse would have been a complete wreck and Shinn would be a fried husk.
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 idiotic 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. Not to mention, she's frankly left alone with few political allies from the other houses...because they all blew themselves up along with her father, and her only emotional support and protection left is Athrun...who himself effectively leaves her to deal with his own leftover issues relapsing. Right then and there, the Seirans break her and almost force her into a marriage where would have been no more than a trophy, were it not for the intervention of Kira. Even then, the only way to save her from a by-then-EA-controlled ORB was to temporarily take her as far away from the land she's responsible for as possible. It's only after she gets a message left behind by her father that she decides to be Orb's ruler as herself.
Shinn trying to use the Destiny Gundam to catch the Infinite Justice's beam sabers makes sense, given he saw the Strike Freedom do the same. What he failed to consider was that the Palma Fiocina is not a substitute for the Beam Shields the Strike Freedom used to catch his Arondight and that unlike the Arondight, the beam sabers had no physical blade to catch.
Even with trauma and guilt from being partially responsible for his PTSD, why is Lacus suddenly hesitant again to give Kira the Strike Freedom when, after the first sortie with the Freedom once more, she seems to be okay with him going out into battle. It seems like she grabbed the Idiot Ball, which is understandable, but there are two things to consider:
First, how are we to assume that it doesn't ache her to see him go out every time and we just don't see it, coz we don't need to see it every time?
More importantly, consider this: He just came to the Eternal's rescue...in the Strike (Rouge)? Wait, why isn't he piloting the Freedom!? That could mean only one thing. The Freedom was destroyed. Hell, it's unlikely they never heard about the news of the Freedom's destruction from their ZAFT informants, but that also Kira is alive but obviously got hurt badly....and now she's about to send him out again after he's had yet another close brush with death, and the Rouge is also getting really trashed out there. Hence he has to assure her again that he'll be okay and he can protect her and everyone else again with his new sword. The presentation is still flawed, but it's easier to swallow in context.
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.
Stellar's death is a familiar situation for Gundam fans, as Shinn isn't the only Gundam leads to suffer this sort of loss. Kamille, Judau, even Kira suffered the same pain, but they had people who cared about them to provide support. All Shinn had were Rey and Durandal, who used the poor kid. He could've been as much a hero as the others, and conversely, they could've become just as consumed by rage as Shinn did.
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.
