What I am proposing is too expansive to be in Ghost Recon Wildlands – but if Ubisoft ever make a sequel or another Far Cry, this could be implemented. In essentials, it is an expansion of the Outpost System from Far Cry.
In essentials, a big flaw in GRW is that we do not feel we affect the world enough. We have turned the Unidad general but it has no effect on how they treat us. We have captured El Muro but it has no effect on the efficiency of SB. We have killed Carl Bookheart but it has no effect on the training on SB.
The solution is obvious. There will be factions on the map. At the start of the game, you have SB, Unidad and Rebels. SB is the largest and SB / Unidad will be at war with Rebels. Getting them to fight against each other in this stage requires more than just starting a fight near their troops.
As you progress, factions start to differ. As El Muro turns on El Sueno he will create a splinter faction that is at war with SB. As influence is lost, the Rebels and Unidad gain ground. Villages may declare their independence etc.
If you captured the Unidad General, Unidad may be more tolerant of you – not chasing or shooting at you unless you shoot first or invade one of their bases. Doing stuff like this will also – of course – affect your standing and fear. If a faction fears you, the LT will be more prone to run at once and their foot soldiers more inclined to just surrender.
If a faction is strong, they can launch many patrols or missions to capture nearby strongpoints meaning you will see what faction is strong in the real world. Lots of help to the rebels may see entire areas in their control. You cannot help the Rebels by forcing a take-over but if you see a large rebel force of APCs and Helis on the way to Firebase Armadillo to capture it, of course you can help.
If a faction is weak, they will be less inclined to chase you, their SAMs and Mortars will not respawn or fire as much and they will have arguably less equipment. A weak faction may also see more random splinter factions who vye for control of a region. Add a story arc to give you the possibility to grant control of the country to Unidad instead of the Rebels (who also may fight or ally depending on story actions) and we will really have the "make them fight each other" mechanic promised.
Of course, if you get bored – the entire system and power balances can be reset from the main menu and now you will not even have the story missions to aid you…