There are multiple ways to take FC2 from a really decent adventure shooter into a AAA masterpiece. Here's a list of everything I can think of.
1. Co-op mode. You think that sniping and fire strategies are fun now? Try doing it with someone you can trust, so you can both watch the magic together. If you can do this via LAN as well as online with microphones, double the fun.
2. Make it so that there's more to do in that massive expanse of wonderful terrain. Make objects more interactive than simply just being destructible. Add people that will help you and neutrals (and develop some of them as real characters with proper acting/writing). Perhaps add a faction that's allied, and make sure their that AI is a match for the enemy. Don't be afraid to kill some off, and don't put it entirely in control of the player - they'll just do what I did with the rescuer buddies in FC2, and save everyone even if it means losing hours of game time. Don't allow people to frustrate themselves in this way.
3. The diamond finding game was fun in and of itself, and so improve it. Make minigames within the game, like the puzzles we see in Half Life 2, or simply put them in even more weird and interesting places. For extra points, implement these minigames into the story in a seamless, non-required fashion. For example: you have to kill x guards in a fort who have a diamond or several diamonds. You want them. Characterise the leader of the guards in a cutscene if the player gets close to the fort in-game to give a feel of the danger. Make him seem like a real badass, and then make him fight like a normal AI enemy, only tougher and/or much cleverer.
4. Remove the malaria. It was just a cheap way to ramp up the tension, and though it may seem essential to the African experience, ask an African and you will probably find that it really isn't, that you've just made a cultural assumption. Instead, ramp up the action in the honest way - by making the enemies actually more determined to deal with just you in a curve of difficulty increasing through the game. Maybe have civilians themselves turn against you if you make a choice that they don't like. In other words, show a real depiction of a divide in whatever cultural setting is chosen.
5. A stylistic flair to sell the game and make us empathetic to the story is sorely needed. I'd suggest taking inspiration from Infamous and having moving, comic-style cut scenes to really pace the mood and help foreshadow coming dangers in the plot. Hire a very good graphic artist and a decent actor for the lead role to give a human face to the player. The silent protagonist might be "you" in some people's eyes, but for popular appeal a developed character is more reliable.
6. Improve the line of sight of AI enemies so that they really cannot see through foliage. Whenever someone can snipe you in the grass in the shade from the sun, you're not considering things like eye contrast when switching from light to dark and the real difficulty of seeing a camouflaged soldier who's trained to stay hidden. And finally...
7. Make stealth more than just what weapons you choose, but a style of gameplay that's fully supported by simple actions like crouching. Add a move to dive to the ground and become even more hidden.
In summary: make it less of a pure shooter/adventure. Characterise. Make the adventure MEAN something to those playing, and improve the gameplay options. That will put spirit into the fight, and make people determined to beat the game, meanwhile enjoying the flow of controls.
