Sewer of Horrors was added as a challenge area for AFTER the Ark, and you'll notice the difficulty between the two, not to mention that Ark can be taken in bits at a time when the Sewers is a marathon run.
As for the early quests, you're pretty free to do them any in order you can. Some quests have better rewards if you have better traits (i.e. higher level) but that all comes out in the wash by the time someone reaches end game stuff.