The Darklord would be Ayavcln the Angel, yeah she started kind of good at first, but she ended up twisted by the end.
The Darklord could be the Eldrazi Emrakul. She's already imprisoned in the moon of Innistrad. Be pretty cool if she continued corrupting the area from there as a "shadow ruler."
I was originally working to adapt the setting using the Original Innistrad block rather than Shadows/Moons because of the tonal shift (the original Innistrad blocks were quite gothic, while latter is more Lovecraftian), and further I wasn't considering the recent ramifications from the newer set (Emakul's imprisonment, Avacyn's death, etc) or the idea of Innistrad "being drawn into" the Mists post Eldritch Moon. To be honest, the idea of having Innistrad fill a Lovecraftian horror domain (and Emrakul its trapped lord) would work far better than I had thought. All you do then is add some mists, sprinkle in the domain prohibition on leaving (all the important walkers are off plane post WotS) and you'd have a good start.