The Mirror Universe is alright for a bit of a jaunt to see how characters we know and love might have been under different circumstances (and only really works if they are well established to begin with). Not sure a series spent jumping from one to the other would work, plus it could get a little confusing from time to time (not to mention its a bit of a rip off of Fringe
As for Section 31, I think that they should just be left alone. From what's been seen to date, its not a large organisation and very few people know of it. Also if its looked at in more depth, it'll lose some of the mystery that makes it an interesting concept.