Reputation is a "passive" but notable statistic. Each time the player completes a faction mission (whether it be done through the Buddy's way or not), or a buddy mission, their reputation increases. This means that APR and UFLL troops step up their game to be better prepared against the player: they have better firearms, snipers may replace their rifles with rocket launchers or mortars, and troops install heavier weaponry on their vehicles (such as replacing the M249 on Assault Trucks to .50 Cals or grenade launchers).
There are five levels of reputation, and they each have noticeable effects not just on enemy awareness, but on their behavior as well. Initially, the player character starts off with a low reputation. Soldiers in ceasefire zones will often harshly remind him of the rules, will make snide remarks as he passes by, threaten the player if he walks into a restricted area, and even push him around should the player agitate a soldier. When in combat, enemies will chatter amongst themselves as to who the player character may be, and goad him into revealing himself.
However, with a higher reputation, soldiers in ceasefire zones will be much friendlier and lenient with the player character, often greeting him. In combat, enemies will begin to become flustered and scared, even going as far as to break down and fear for their lives. Sometimes, though rarely, they also perform tactical retreat, and try flanking the player from a distance.