If you follow the classics, then Dresden will see three major changes --- all changes that make for a very painful realization for Dresden.
1) One close ally who is now an enemy
2) One deadly enemy who must be an ally
3) One treasured companion was dead is now alive
4) One friend who is changed for the worse
5) Someone new who he learns a great deal about --- so that he can show off in a later book
The ally that is an enemy is almost certainly Michael, but honestly that is probably too simple as a Knight of the Cross would be able to tell that this Dresden is now their Dresden. I would argue that the ally who is now an enemy is Murphy - which also nicely ties up #3 as well. And Murphy would be a very dangerous foe for Dresden for many reasons. You can make the case that a Susan as Red Court vamp would make a good enemy as well, but it feels weaker.
The enemy who may be an ally. Again the obvious answer is Marcone, but also again that is too simple. To really make this hurt, the ally has to be a serious enemy. That means you are looking at Lashiel or Nickodemus - both would make very painful allies. Other possibilities (Maeve, Lily, Merlin, Red King -- simply do not have the emotional connection to make this alliance BURN Dresden's soul.
Treasured companion now alive is obviously Susan or Murphy - and you have already read why I think it would be Murphy.
Friend changed for the worse is most obviously Molly, except the author has already put Dresden through a lot of heartache related to Molly. A case can be made that Charity could be the one that turned in a dark direction if the change resulted in Michael's death, especially if Dresden is at fault.
Somebody new is pure speculation, but I think this would be a great book to tell us a lot about the federal agency focused on the supernatural. And the payback in later books when Dresden shows off would be golden.
