Now I took a nice bath and sorted out a few thoughts in my head.
So, basic gameplay is similar to Peace Walker and XCOM, you have a map and you choose mission. Except that instead of only a 2D map you have an actual 3D world, where everything is connected. The catch is that there isn't a free roam mode, and during missions you can't just wander around, otherwise bad things will happen o you.
E.g.: if you infiltrate an enemy base, then you must take a whole squad, to replace an enemy unit. If you run out with one of your men on the main gate, then people will think that you are a deserter. even if you survive, political officers will torture the rest of your squad to death to figure out what happened, and will learn everything about you.
Now, you mainly interact with the world through missions, but what else is there? And how would the combat look like? Well, look up two real guerrilla wars set in Africa for inspiration:
en.wikipedia.org/wiki/East_African_Campaign_(World_War_I)
en.wikipedia.org/wiki/Rhodesian_Bush_War
You'd mostly play hide and seek in the front line, between two (or maybe later on three) gigantic armies. Your best bet is that they are too busy with each other to even notice you until it's too late. So you have to micro-manage your men, set up small bases and supply catches everywhere, manage the guard duties and the people in general. You could pretty easily avoid everything in the beginning of the game. But then you will just run out of food, the front line will move over you, or something else happens. Therefore you are forced o actually take risks and confront the enemy, just to take what you need for survival. Now, the game should mostly tell a story, so you shouldn't waste your time with hiding from guards just to steal three cans of tuna.
Here comes the basic difference between this game and MGS: to infiltrate an enemy base, you have to observe it, and then impersonate someone or something to get what you need.
E.g.: you kidnap an officer from a base, dress up one of your men as him, and use him to order a wagon full of cans to be sent to an other base. He will be in charge of that small caravan, you attack them, and then your "officer" gives an order to the people under him to retreat. Then he disappears and you place the corpse of the original officer in the site of the ambush. Now the enemy might find it strange that the officer disappeared and reappeared with orders that make no sense, but if you time around the time of a major enemy attack, then they will be too busy to even notice.
And how do you time it with an enemy attack? By infiltrating the enemy headquarters. Maybe knock out a few guards for an hour during a night, and send in your men to steal some plans. The guards will be either too scared from the political officers to even mention what happened, so nobody notices that a few pages disappeared. Or they notice it, think that the guards were actually enemy spies, and execute them. In either case, nobody will care about you, because they are preparing for a major attack.
Now you can see that the idea is about getting a lot of intel in different ways, and making plans based on them. But an other driving force should be the story, and it should unveil as you get intel. E.g. a floating fortress full of nukes will be deployed in the next landing, so you must get there and infiltrate that somehow, then fire the nukes at a major city. It takes several steps, all of them involving ambushes, kidnappings and impersonating people.
Now, as you do your stuff the higher ups will eventually notice that something isn't kosher. So they will send some special response teams who can quickly appear at the sie of your ambush. They also tighten the defences of their bases, e.g. more guards, more passwords.
And last, but not least: they will try to counter-infiltrate your group. So now you even have to be suspicious of new recruits.
How is it so far? Sounds like a game?