This troper once wondered why Kojima decided to tone down the game for the children. (and kept telling the press about it) AI boss fights and less gore aside, considering that the main topic is peace, it became easier to see why.
Many people question how the mission ranking goes down when people (and the Monster Hunter creatures for some reason) are killed. Simple explanation? The game is titled Metal Gear Solid: PEACE Walker for a reason, as (besides Peace Walker being the game's Disc One Final Boss) peace is one of the main themes of the game.
The SUG assault rifle has a scope on it, but aims like any other assault rifle in the game (ie. using the over the shoulder camera). It's more than likely that Snake (or whichever of his MSF soldiers) is aiming using the iron sights mounted on top of the scope.
Actually, the scope used by the AUG/SUG provides only with 1.5x magnification, and in overall works a bit more like a reflex sight than a traditional scope. Perhaps this adds to the in-game weapon's ease of use and aiming.
Much has been said about how TX-55 is so 'outdated' compared to the canonically preceding ZEKE, and a good part of this always seems to go towards the fact that the TX-55 is much smaller in size than it. However, is this really a sign of older technology... or actually the contrary? For starters, while being smaller, it still nonetheless possesses not one but two nuclear launchers. That alone would make it more advanced in the main role of the Metal Gears, that's it, of a nuclear weapon. A more compact size would also be translated in cheaper price, and thus easier mass-production. Oh, and it would also be able to aid infantry in places where ZEKE would be too large to go in, thus also fullfilling Granin's original idea of a bipedal tank as well. All this could apply to D, as well. Strangelove, in one of the cassette tapes, mentioned something about how scientists are starting to find ways to miniaturize robotics as technologies advance. Maybe this could be a very subtle hint at how actually more advanced TX-55 is, at least in some aspects?
Of course, it seems to matter less considering that Zeke will presumably be destroyed in Metal Gear Solid V
Despite the fact that Paz is a double agent with a different nationality than what's said, she still speaks with an accent and uses a few phrases native to Costa Rica in the final boss fight, despite the fact that she's dropping the facade. Her diary shows her warming up to Motherbase and wishing she could keep up the facade a little longer. It might be a sign of her wanting to stay as Paz and not be Pacifica anymore.
When she confronts Big Boss, she predicts his and Outer Heaven's statuses as the villains in the original Metal Gear games as carried out by the new world order. In the stylised comicbook cutscene, Big Boss's profile briefly takes the poised, combat ready pose of a Metal Gear. His legs especially are bent and ready to fight, being particularly reminiscent of their legs. Effective use of the Rule of Symbolism and a taste of the future.
There's another reason why Snake/Big Boss didn't really buy the "professor's" cover story about being part of the UN's University of Peace in Costa Rica: although the country actually did abandon an armed military by the time the game takes place, the university didn't exist in 1974. It would be another five years before it was even founded.
Two gameplay quirks can be nicely interpreted for Big Boss and his developing private army. When he's taken out of action for example by being held in the prison cell or engaged fighting Peace Walker, does the day to day activity at Mother Base stop? Not at all. You're still free to do everything you usually can, just not controlling him. In particular you can deploy soldiers to other missions e.g. to support him on his main operations. Which brings me to my next point. The codec team refer to you as Snake even while playing as other soldiers. In other games this would be regarded as a minor oversight for not referring to them as something else. But here, taken in conjunction with the first observation, it all makes sense. Big Boss is building a big, capable force in MSF/Outer Heaven, and deeply respects anyone who joins. Anybody worthy to serve (particularly in frontline sneaking/combat missions) is worthy of the coveted title "Snake" while putting their life on the line. And he might be the co-leader with Miller, but he's ultimately just one cog in the well oiled MSF machine. It's the whole which makes it so effective, not just his command/actions in missions. A great leader, indeed.
In one of Huey's briefing files, Huey explains that Peace Walker was equipped with a hydrogen bomb (specifically the large, "Death Star"-esque orb on top), larger both in size and magnitude than even the Soviet Union's Tsar Bomba. Huey explains that the reason why it has it on there is basically so that, if it needs to do so, it can infiltrate a nation and basically self destruct and take the nation with it. Now, recall earlier that Huey mentioned that Coldman planned on mass producing it throughout Central America, something that Hot Coldman later states as well, and you'll gain the realization that, if the mass production actually happened, and if Hot Coldman, or heck, any madman controlling them were to decide to activate their self destruct option, that means Central America would also be wiped off the map.