Army of Two/WMG

Salem and Rios are a gay couple
This may be more of a "no, really, you think?" than a WMG, but since there's no actual confirmation in the game, it seems appropriate.

Salem and Rios are very tightly knit, to the point where they're probably around each other out of missions nearly as much as in them. Neither of them makes an attempt to hit on the female lead whom they interact with on a daily basis, and in fact, she tends to go back and forth with them on the nickname 'hun,' but it's always a very tongue-in-cheek delivery. The fact that she rolls her eyes at their fratboy-ish behavior and closes a door in their faces when they first meet suggests we're not meant to even think either of them are a good fit for her.

Given the setting and his behavior otherwise, it's thematically bizarre that Salem never brags about his sex life. Rios, being the more down-to-earth of the two, would probably not do this at all and is often wondering how Salem can have such a short attention span on a battlefield; the one thing Rios goes into a tangent with is a concern for Salem's personal life, suggesting that Salem's well-being is important to him. Rios also tends to have oddly tender one-liners when reviving Salem, and his lines signaling to a player-controlled Salem that he's low on health are delivered with a tone suggesting as much emotional need for backup from Salem as physical.

Perhaps the most telling, if also the most subtle suggestion of this comes in the form of dialog during the China mission, after and their morals clash:

(Paraphrased) "Salem: We could just not try to make all of this right, let the conspirators go, and maybe even make money off of the conspiracy by helping it out. Rios: No, we're going to do the right thing and stop them or die trying. Salem: Okay."

Salem is noted to have grown up in a gang to the point where he was put into a "choose prison or the military" scenario, and that, as a result, he sees little value in common decency and even less value in being financially responsible. It's noted several times, even right before this dialog occurs, that he'll do anything to make a quick buck for the support of his lifestyle. This scene essentially amounts to Salem willingly setting the basic principles he lives his life by completely aside because Rios tells him he's wrong. People are simply unwilling and often downright unable to do this even when presented with the most pure moralities as motivation, and Salem is clearly not considerate of pure morality. He does this because he cares what Rios thinks about him on a level deeper than friendship. While it could be argued that Salem simply sees their situation as hopeless if he doesn't have Rios for backup, it could also be argued that he's not the type of person who would actually think of this until its too late. If anything, a refusal to go along with Rios in this scenario would probably result in Rios pointing this out to him.

Finally, the prequel to the game depicts Rios with a girlfriend and a daughter, which seems to torpedo this whole idea...until it gets to the part about how they've tried to marry several times only for Rios to go on a mission (with Salem) instead. The final scene in the book has Rios and Salem asking for time off from their boss, so they can vacation in Hawaii together.
 * In one of the cinematics, Salem is shown trying (and failing) to hit on the girl. Though it is possible he's bi.


 * Salem is either bi or straight. He considers a strip club a palace.

Alternatively, they're Heterosexual Life Partners.

Clyde is an Immortal.
He, and they Never Found the Body after he. The fact that Salem and Rios briefly discuss how that is even less survivable but they have no way of knowing for sure suggests the devs are planning an Untwist in the form of bringing him back in a sequel. Furthermore, the Highlander TV series, on several occasions, showed that immortals can very easily slip into various degrees of batshittery either close to or a dead ringer for his issues depending on the life they lived as a mortal, the circumstances of their death, and their ability, or lack thereof, to handle immortality and the Game responsibly.
 * Alternately, the plane crash was his first death, leading him to return increasingly annoyed.

This game is a prequel to Metal Gear Solid 4.
PMCs beginning to replace the regular military? Oh yea.
 * The failure of the bill that would've privatized the US military inadvertently leads to the United States' weakened position circa Guns of the Patriots, with the still-growing PMCs out-pacing state militaries. Salem and Rios, not really in a position to see the way things are going like Snake and Otacon are, happily retire after being bought out by Outer Heaven and renamed Ravensword. Former SSC employees on the run jump ship to Praying Mantis in the UK.