I was saying last night, I can only imagine how good a game like this could be if somebody took the base and its good bits, and injected a bit of genius into it. I really enjoy it as is, even with its janky bits and other unpleasantness, but it's an unusually enjoyable 'B tier' game (I normally hate all this 'GOAT', 'tier' stuff GAF recourses to, but here it's useful). A dash of Kojima (although keep him away from story, can't stand that nonsense) or w/e and boom.
For instance, I was thinking that the civilians could be better utilised,on multiple levels. Given that Santa Blanca have rather egregiously taken over the country and are terrorising the populace, it's not like the population should love them. But they should react more to you as also-invaders, even if your purpose (if not your methods) is benign (or can be defended as such). I wouldn't want it too political, but I like the idea that if you're in a civ area, you might need to be much more careful - e.g. your clothes matter, putting your gun away matters more (it's currently pretty much a nice roleplay touch, rather than a gameplay/system thing), too much destruction and the populace turn on you. Not violently, but perhaps it could have been the case that if you keep them on side they provided you with resources, and losing them in a region would reduce your ability to take on the cartel and Unidad, and reduce rebel support for you. Then you might have to win them back by 'good deeds' (albeit handled far better than it likely would be, i.e. 'save a hostage to win +10 popularity points!' nonsense).
It would clash with the reckless possibilities of the game to an extent, but it would be kinda cool. Perhaps it would work best tied into emphasis on surviving off-grid. I wouldn't want a game that cripples you due to lack of food or sleep, say, but a touch of survival elements, of living in the wilds, would be a really interesting possibility. Keeping the population on side would help this, but sometimes you'd face the choice of causing destruction at the cost of later sustainability, and it'd be a more interesting moral and political context than 'hoorah, we're here to save you, woops I shot one, be careful guys!'.
/rambles