WMG: Area 88

Greg intentionally destroyed Gold's documents.
When Greg discovered and destroyed the Arabic documents at Gold's crash site, he wasn't simply holding the idiot ball. He knew that the documents could give the pro-monarchy forces a decisive edge and possibly end the war, thereby putting him out of a job. He intentionally destroyed the documents so that the Asran civil war would continue, providing him with continued employment as a mercenary.

Shin's amnesia at the end of the manga was an act.
Shin feared that Ryoko wouldn't take him back after he broke her heart, so he pretended to have amnesia to play on her sympathy.

Saki's private soldiers in the manga were beards.
Saki was asexual, suggested by the fact that he never had a love interest or showed attraction to anyone in any continuity. Fearing that others would presume he was gay, he hired four beautiful women to be his bodyguards, hoping observers would make assumptions. The bodyguards didn't say much, mainly because they didn't want to accidentally give away Saki's asexuality or their beard status.

Ryoko suffers from borderline personality disorder in the manga and OVA.
Where to start? She idealizes Shin despite evidence to the contrary, she's impulsive, she has intense moods, and she attempts suicide in manga that did not make it stateside. In her quest to reunite with Shin, she seems unconcerned about how her actions will impact her father, Taeko, or Josie, suggesting an empathy deficit. When she and Shin are temporarily reunited later in the manga, the relationship is intense but ultimately unstable. Her obsession with Shin could be interpreted as an attempt to avoid perceived abandonment, and/or an attempt to soothe some inner emptiness. When one looks at Ryoko's behavior as a whole, she could plausibly be a BPD sufferer.

Sawa is one of the Observers
He's bald, he always wears a black suit and tie, and he appears at just the right time to save Saki's life. Maybe he's protecting Saki to make sure that certain events occur in the timestream.

Kanzaki aerial duel with Shin was intended as suicide
At the end of the manga, after Project 4 collapsed, Kanzaki challenged Shin to an aerial duel. During the duel, Kanzaki told Shin about his mother's suicide, as well as her murder of Shin's parents. Kanzaki may have brought this up because he wanted to be with them in death. Kanzaki also chose to duel with a man who had years of combat experience in a brutal civil war, so he had to have known that his odds of beating Shin were nil. In short, Kanzaki may have wanted to die at Shin's hands, or at least go out in a murder-suicide, since he had nothing more to live for.

Saki knows full well that Shin isn't at Area 88 for the same reason as everyone else. The Escape Killer trio didn't really need to confront Shin and issue a challenge. It almost looked as if they were actively discouraging him.
Lead Escape Killer: "We understand your situation, but this is not the answer"
Escape Killer #2: "You can never escape from here."
Escape Killer #3: "No one in the Middle East has ever made it past us. Care to try your luck?"
  • They could have just stayed hidden and allowed him to take off so that they could follow him unexpectedly and shoot him down. Presumably, this is the way that they would usually work if they expect to make any money from hunting deserters.
  • This alleged desertion attempt was happening in the dead of morning. It was strange for everyone else to show up at that moment. First Mick, revealing that he finally remembered who these three guys are. Then Greg and the rest of the pilots, who just happened to show up to participate in threatening to beat down the Escape Killers. And finally Saki, who tells the three pilots to leave and report this incident to headquarters stating that there are no deserters here.
  • There is no questioning towards Shin as to why he was geared up for takeoff with no mission. And when Shin appears as if he's beginning to confess his true intentions, Saki and Mick cut him off and instead assure him that he will get home.
  • Most likely, Mick remembered much earlier and informed everyone else, except Saki, who may have known why they were there. Mick seems relieved that it turned out that Saki didn't call for them, after all. And Saki reassures that he would not hire "Escape Killers"