Judging just from what the Reputation screen looks like, it seems like we'll be able to take random jobs from different factions. This is nothing new in the world of MMORPGs, pretty standard actually. My guess is that's how most of the side missions will be handled. That's the feeling I got every time I did one of the current side missions and Capt Grant says "this isn't something a soldier can do". A lot of the NPCs you rescue in the random world missions also say things along the line of "I'll make sure so-and-so hears about this".