question about bonuses during missions

does completing every bonus effect the game in any way is it just for the exp?
there are alot of missions where the bonus just doesnt seem worth it, like the 5 chosen being selected by the pyramid eye.

my advice - save the bonuses till your level 20 and trying to get xp for skill points. That way you can get 24K experience right there and then... which equates to 1 level and thus 1 skill point..

But apart from the experience gained there doesn't seem to be any real reason for the bonuses. They are just side bonuses which don't effect the main storyline.