In the existing game there's an escalation of your bullet spongy-ness to enemy level complexity, this naturally happens as you progress through the map. I would remove the bullet resistance and player levels and go with an almost totally real health experience and I'd try and blend more Hitman style recon elements into the game.
Like being able to drive around, or walk around plain close with no weapons to recon places, and have to talk with locals about the enemy in detail. I'd also preserve progress, if you free an area the enemy should become less of a presence and the freedom fighters should take charge.