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.