What does character choice affect?
Character selection will only impact which buddies are available (you can't be a buddy to yourself, for example) and the order in which they appear. Each buddy also has different side quests available, so if you pick a specific character you won't get 'asked' to do those missions.
Far Cry 2 Wiki example: http://farcry.wikia.com/wiki/Marty_Alencar