Full Metal Panic!/WMG

Sousuke is actually a Whispered that just hasn't awakened.
In the novel backstory "Kyokuhoku Kara no Koe," which details Kalinin and Sousuke's long, fateful past together, Kalinin puzzles a bit over Sousuke's mysterious background. Huddled together under a blanket (inside the crashed plane) was a man, woman, and young child. The man (who was around the same age as the woman) was already dead, and he is never identified (so whether or not he's Sousuke's father is undecided). The woman, however, calls Sousuke her child, and is described in similar terms as Sousuke (including her calm, Dissonant Serenity at falling to her death, and being described as surreally beautiful the way she doesn't care about her impending death). In fact, it's pretty certain that she is his mother, considering that in Burning One Man Force Sousuke remembers her as his mother. Now, the strange part comes from here: Sousuke's real name is most probably not Sagara Sousuke. That was just the name scribbled on the back of his clothes with a felt tip pen. And, there's no record of his being a passenger on the plane. Could it be that the plane crash wasn't a coincidence, and it actually was tied in to Sousuke possibly being a Whispered? What other reason would there be for his mother to make him go under an assumed name? Kalinin addressed this issue, but said that Sousuke never corrected him when he addressed him by that name - is it possible that Sousuke was instructed by his mother (and the man with them) to just go along with people calling him that (maybe for his own safety)? Also, isn't Sousuke around the same age as all the other Whispereds? Being 16 years old. Not to mention that, even without undergoing tests to "awaken," he's shown to already be a Teen Genius when it comes to Arm Slaves and artillery and explosives. It might also explain why so many Whispereds are attracted to him.
 * Either that or he already wakened, and somehow lost his "Whispered" status (brain damage, perhaps, due to overzealous testing, which resulted in the creation of the basic AS, which is why he's such a great pilot). This would explain why.
 * Note also that Sousuke is almost failing literature and history, which are cultural subjects. In contrast, he seems to have no issues with his science or math (the typical Whispered subjects) despite the many factors that should adversely affect 'all' his schooling.

Gauron is still alive.
Or rather Sousuke successfully killed killed Gauron nearly every time they fought. The reason, the original Gauron is alive but not well. With cancer consuming his body, Gauron, armed with not yet revealed black technology, is cloning himself over an over again in order to keep fighting. My reason for proposing this is that the theory that Gauron has protected himself with the Llambda Driver every time his AS was destroyed by Sousuke doesn't hold water. The basic reason for this is that as Chidori explains during Sousuke's first AS battle with Gauron is that the Llambda Driver's defensive capability relies on the survival instinct of its operator. Gauron, who possesses a suicidal urge and reckless abandon for even his own life is able to use the Lllambda Driver for basic defense, but lacks the necessary survival instinct to use the Llambda Driver to shield his own life (rather than acting as a shield for his mech so he can keep fighting). Part of the reason for this suicidal recklessness is that all of Gauron's clones are aware of the fact that they are clones but consider themselves extensions of the original Gauron's life. On top of that, Gauron is somehow able to absorb the experiences and memories of his clones into himself so that he can impart that to future clones. This explains Gauron's ability to survive unsurvivable situations.
 * Or he's going to come back as a cyborg zombie. That plugs directly into his AS's interface. Especially if Amalgam got their hands on a Whispered with knowledge of advanced cybernetic grafts/implants.
 * Unless they can salvage his body a la Big Boss after killing himself by blowing up his own apartment, he's dead for good.

Yoko Wakana has a sister
By the name of Revy, they're both gun happy, somewhat nuts, and have a really similar smile. I'm guessing Yoko dyed her hair to stand out a little bit more.

Mithril is part of the UN
or does a lot of work for them. I have only seen the anime, but it otherwise doesn't make sense to me how they get enough funding to field equipment a decade more advanced than anyone else. A significant portion of what they do is stop wars and fight terrorists, something the UN is supposed to be involved with (to the best of my knowledge). Also, they had UN uniforms ready to use at the drop of a hat, which would likely imply that they had done something along those lines before, and I imagine that impersonating a UN soldier is something the UN would be rather against. Even though they are technically a mercenary organization, I think that, at the very least, most of their missions come from the UN.
 * It's the latter. They are a covert anti-terrorist mercenary org after all.
 * That’s what the United Nations wants you to think!
 * Jossed on the former. The latter is pretty much confirmed.
 * In the novels, Mithril impersonates soldiers of various nations, which also includes pretending to be American soldiers. So they aren't part of the UN, but it's possible for Mithril to "assist" the UN. Although they try to be neutral...

The Lambda Driver runs on Spiral Power
Think about it: It's a mech that has the ability to break the laws of physics, but ONLY when the pilot in is the right mental state.
 * Or its part of the super robot family of green, glowing energy that includes Spiral Power, G-Stone and Getter Rays.

Another Guess Involving Gauron being Still Alive
Gauron survives Sosuke shooting him in the head while he is his quadamputative state by having a bullet which was already lodged in his skull (from the time Sosuke tried to kill him with a sniper's rifle.) block the bullet that Sosuke fires at him

Sousuke has Asperger's syndrome
If he does have Asperger's, he must be extremely high-functioning, but he does seem to have some of the symptoms:
 * Obsessive interests at the expense of others. He builds up intense knowledge of all things military, and I don't think it's just because he was raised as a soldier.
 * Difficulty with romantic relationships. His obsession with military stuff overlaps with this. He also mistakes "kissing" as a euphemism for CPR. Asperger's can do these things. He also generally has trouble expressing romantic feelings -- Sousuke can be very stoic. He also seems uncomfortable with sexuality at times.
 * None of this necessarily indicates Asperger's Syndrome. A more likely hypothesis is that Sousuke was a child soldier (for that matter, he still is a child soldier), who has never had a chance to learn how to socialize in non-military ways. His skills are literally completely focused on the military.

Gauron is an Immortal
He may not be able to regenerate missing body parts very quickly, but since none of his reported deaths in the series involved cutting his head off, he isn't dead yet.