From the All That Glitters episode: Exactly how were the pilots searching for the gold expecting to bring it all back to the base? Or, for that matter, land safely without a runway?
A far more glaring one springs to mind: Why didn't Shin ever pick up a phone and call Ryouko? It's never explained in the 2004 series at least.
Probably 'cause the Asranian military may monitor all calls out of Area 88. Since he can't leave 'til he pays $1 million bucks...
Even if they're monitoring it, at the very least he can tell her "Hey I'm alive, don't marry that ass!" And if it's $1 mil they want, Ryouko can help him work it out.
Also, Shin knew that Kanzaki was dangerous because it was Kanzaki who tricked him into signing a mercenary contract. Why didn't he warn Ryoko about Kanzaki?
Probably to avoid putting her in danger.
In the manga and OVA, Ryoko is determined to free Shin from servitude at Area 88. Why didn't she ever stops to wonder why he was there in the first place?
Until Kanzaki started really moving in on her, Ryouko had no reason to believe that he was up to no good or that he sold Shin off to the Asran military. After all, Shin and Kanzaki were incredibly close childhood friends. Not even Shin knew the kind of person Kanzaki was until he woke up with a mercenary contract.
She didn't necessarily need to suspect Kanzaki. It was just strange that, upon learning that Shin was at Area 88, she found nothing odd about a man with a promising future vanishing and resurfacing as a mercenary in the north Africa.
Why would the Asran air force take Shin, even if his signature was on a mercenary contract? He had no military experience and was fresh out of flight school, so in theory he wouldn't have made a good mercenary.
Simple. They hired foreign mercenaries to do all the dirty work they didn't want their own army doing. As both the manga and anime illustrates a LOT of guys die on every mission. But the contracts always promise a crapton of money, so there's no shortage of people signing up. Not to mention a great deal of the pilots are either criminals on the run or veterans who can't fit into civilian life. In short, Asran has no problem sacrificing foreign pilots so long as it keeps their own soldiers off the battlefield.
In the manga, Kanzaki meets with Farina to put a hit out on Shin. Charlie is dispatched to Area 88 to kill Shin, but crashes his jet and dies. A few issues later, Shin crashes in the desert and is taken captive on board Farina's land carrier. Farina knows who Shin is, but does not kill Shin, and even gives him medical treatment for his injuries. Why didn't Farina kill Shin, under the terms of his agreement with Kanzaki?
In the manga, Greg finds anti-government documents near the crash site of Gold's aircraft, but he cannot read them because they're in Arabic. Toward the end of the manga, however, he communicates with a frightened Asranian child. When did he learn Arabic?
Having worked for Asran for so long, all of the mercenaries are bound to pick up on the Arabic dialect. As for why Greg can't read Arabic, knowing a language doesn't guarantee literacy. Many people in the world are fluent in one or more language but can't read said language.
In the manga, Farina commissions the construction of a massive land carrier. Once the carrier is in Asran, Farina oversees its attacks on pro-government forces. How on earth did his company transport such a huge monstrosity across the Mediterranean Sea and foreign borders without drawing any attention? For that matter, how did he transport a nuclear weapon for the land carrier without drawing attention?
Exactly where are the two sides of Asran's civil war getting the money to continue the armed conflict? Mercenaries, equipment, and arms are expensive, and Asran does not export its oil, as Saki states in the manga. If Asran can't afford to provide more than a third-world existence to its citizens, how can it afford materials and men for a civil war?
Since the motivation for the civil war appears to be whether or not they should allow foreign investors to come in and drill for oil, the rebels are probably getting secret funding from countries who want to drill. With the imperial side, it's not really surprising to see their army fully equipped. Even in real life a lot of third-world countries have a fully stocked military because they tend to funnel most of their money and resources into the military. That's probably what the Asran government has been doing to fight the rebels.
Why does Area 88 seem to have such poor communication with Asranian military headquarters in the manga? When Mario Bandini and the Enforcers/Escape Killers land at Area 88, Saki is unaware of who they are and was not expecting their arrival. How can Area 88 maintain its security if military headquarters doesn't alert them to visitors, and outsiders can breach the base with impunity?
In the manga, Saki doesn't run a very tight ship at Area 88. During the Wolf Pack crisis, he allows his elite team of mercenaries to manipulate him into giving them free jets and equipment in exchange for obeying orders implicitly, which is supposed to be their job. When Shin menaces a civilian plane and attacks him during a psychotic episode, Saki's only response is to keep Shin in a holding cell for a few days and release him without incident. He can't or won't maintain good communication with Asranian military headquarters, as evidenced by his surprise at the arrival of Mario and the Enforcers/Escape Killers. Saki demonstrates a lack of professionalism in his management of Area 88, so why is he allowed to keep his job? Is the Asranian military willing to turn a blind eye to all this because Area 88 is doing so much damage to the anti-government forces? Is he untouchable because he's an Asranian prince and the nephew of King Zak? Or is the Asranian military just that unprofessional?
At the end of the manga, Shin has amnesia and doesn't remember Kanzaki's betrayal or his time at Area 88. As revealed in his conversation with Ryoko, he thinks he's still a student pilot, and that his combat injuries were caused by an accidental crash. Doesn't Shin find it odd that he's in North Africa instead of France, that he and Ryoko have aged several years, and that he likely has scars from prior combat injuries that he can't explain? Since it's heavily implied that Ryoko never told him the truth, how on earth did she spin this?