To me, it seems like something of a faction choice: By siding with one or the other fairly early on, you play through a "completely different game", depending on faction. The factions probably have different sidequests, main quest, and so on. However, I'm sure they'll also share some quests (quests that simply are not affected by whether or not you're this or that faction).
It's probably something similar to Gothic 1, with the various camps, but perhaps with a bit more variety (in G1 the main quest turned out to be mostly the same once you got past a certain point). Also, it seems like the choice is made near the start in Risen, unlike in G1 where you do a bunch of neutral quests first.