Some more ideas:
*In the beginning, you are given a choice (whether explicit or implicit) whether to join the resistance or not. If you do, you are immediately put into an extremely difficult situation, say, facing down a platoon of heavily armed and armored soldiers while holding a baseball bat, are killed, and have to start the game over (which won't be frustrating because you're only one or two minutes in). You then, depending on how quickly you learn, either do the same thing over again looking for the soldiers' glowing red vulnerable point (which of course does not exist), or choose to save your hide and then begin some sort of survival phase.
*There is some sort of survival phase. This phase consists neither of you fighting enemy soldiers as part of the resistance nor of you desperately trying to escape a live fire zone. Instead, it consists of you trying to survive in an occupied region with a high level of ongoing violence ? trying to find food, supplies, work, and so on. I don't see the work as being implemented with minigames, though... Perhaps you are some sort of artisan, and need to procure supplies in order to produce your wares. This means going to the store, dodging patrols along the way (since those sometimes result in crossfire situations that can very easily get you killed, and since there's also the danger of you being misidentified and fired upon), but after one or two trips, you find that the store is running out of supplies, and need to either get in contact with the black market, or find some other sort of work, perhaps with the occupiers, perhaps with the resistance, or perhaps with nobody, choosing instead a life of crime. From there, the plot would thicken, and would also branch, with multiple very different storylines that depend on the choices you make. It would however still be possible to change careers. Perhaps you help to arm the resistance but also engage in petty theft; perhaps you start out working with one faction but then grow disgusted at their methods and attempt to switch, (hopefully) overcoming the other faction's suspicions (depending on how much they know), and earning the other's enmity (again, depending on how much they know).
*There is a larger plot, involving the machinations of superpowers, leaders of the resistance, and so on and so forth, but it is shadowy, distant, and imperfectly understood by Joe Schmuck the protagonist. Getting news ? particularly reliable news ? would be extremely difficult following the general breakdown of communications that accompanied the invasion, but from time to time distant events would make their influences felt in very immediate ways, such as dramatic increases (or decreases) in the number of patrols, changes in their behavior and demeanor, cities falling into insurgent hands, offensives being launched, etc. Rumors would fly, and news would frequently be contradictory. The news media, of course, would have no idea what things were actually like on the ground.
*There is moral ambiguity, and lots of it. No side, be it the occupiers, the resistance, organized crime, whatever, is monolithic. Most of the occupiers truly believe that their cause is just, and most of them bear no ill will towards the populace, at least at first. However, their tactics still result in large numbers of civilian casualties (though this may change depending on the larger plot, of which the player will be partially unaware, though they may be filled in after the fact). Because of the high casualties, and outrage at the loss of sovereignty, a popular insurgency arises, then, because of anger over their fallen comrades, the occupiers' attitude towards the populace hardens. This leads to more civilian casualties and infringements on civil liberties, which strengthens the resistance. As the resistance grows, though, factionalism increases; some insurgents care about civilian casualties more than others, and enmities develop (though the player might not know about them). As the plot progresses, the country slips towards civil war, the occupation's hold on areas slips, those areas experience more crime and fighting between rival groups, and the occupation increasingly brings in heavy weapons. Everyone has the potential to be an enemy, yet no one (or almost no one) is overtly evil.
*There is a sophisticated system for conversations, perhaps based on Alpha Protocol's (which I really liked, even though the rest of the game was problematic), and all conversations are connected with both each other and the looming specter of the plot. You can't talk directly to occupying soldiers (who don't speak the local language), but you can talk to collaborators to find out what they're thinking. You must be careful, though, not to arouse too much suspicion; this can partly be averted by talking to multiple collaborators, but they might speak to each other when you're not there, and word of your inquisitiveness might spread. None of this is heavy handed, though; instead it is all handled smoothly and organically. Every character is voice acted, and voice acted well. Characters are memorable and compelling, without seeming contrived. Trumpets sound from heaven, and cheerful servants bring me cheesecake.
*Death for the player is not permanent. Death for their family and friends is. There's no "your daughter got killed, you lose." Instead, it's "your daughter got killed, now what?"
*Health packs are not conveniently scattered all over the landscape, and your character is not secretly Wolverine. Instead, if your character gets injured, they stay injured for quite some time, perhaps permanently, and must deal with the injury as appropriate. This is important because injuries are an important part of occupations, but implementing it would be very difficult.
