Far Cry 2 also had the buddies system, which I have missed greatly in every entry since. Far Cry 3 was an awesome game but I do wish the series after had taken more inspiration from 2 and less from 3. Subverting missions and then losing your favorite buddy in a firefight is an experience unlike anything in the rest of the series.
Ah yes, the buddy thing was pretty neat, and in some ways your choices even from your starting character had some meaning. They could have done so much more with that by now.