Such a fun topic!!

Harry -  Denarian and completely simpatico with Lasciel.
Marcone - Knight of the Cross (This is just too good not to use).
Murphy - Dead from the Loup Garou.
Maggie - No Maggie, Harry didn't show up in time.
Susan - Still alive and still an unturned Red Court vamp, will never forgive Harry for saving Maggie (hey, how else to torture Harry even more?)
Michael - Black Court vamp (such a great idea)
Molly - a crazy mind controlling bad guy still on the run from the white council
Morgan - still dead, but took all the blame
Peabody - still slowly infecting the White Council's minds with his special ink
The Archive - I don't know how she'd be different, but she'd be an interesting character in the story.
Rudolph is a good guy and is trying to help Harry (talk about torture)
The ThreeEye drug problem is out of control in Chicago...

The Three Eye problem has to be solved and Murphy cannot be dead from the Loup Garou. The divergence happens after those events.

I think it's an upcoming plot point. Bob is not aware of Bonea. Alfred, Molly, Mab and Maggie are the only ones aware of Bonea. Molly isn't aware of Bob. The last is important because Mab is on the lookout for our favorite skull-resident letch.

No. Molly is the firstborn.

In Storm Front, Marcone is an established underground boss with construction, gambling rackets, drugs and presumably, prostitution. Harry Dresden is Chicago's only practicing wizard and a consultant for Chicago Police Department's Special Investigations unit. On Dresden's way back from consulting on a crime scene where one of Marcone's henchmen was assissinated using magic, Marcone swoops down in his limo, picks up Dresden and takes his measure in a soulgaze without flinching and tries to warn him off the case.

This doesn't strike me as the actions of someone who is completely ignorant of magic.

First, iron-hearted or not, a soulgaze is supposed to be a moment of shocking intimacy.

Second, the reader is ignorant that Tommy Tom is involved with Victor Sells' rituals to create Three-Eye at the point where he's dead and introduced as one of Marcone's henchmen.

Dresden shuts down Sells, who dies in the process and cannot turn witness or testify to the White Council or the Chicago PD who else was involved in the Three-Eye ring.

In Fool Moon, Marcone's business partner and one of his henchmen wind up dead at the hands of a werewolf.

Harry, while talking to a demon for information on the Loup-Garou, guess that Marcone has his hands on a pack of werewolves. There are only two werewolf packs in Chicago, the Alphas, who would never work for Marcone, and the Street Wolves, a gang of lycanthropes, humans possessed by wild spirits.

Then Marcone, dues to shady business dealing winds up in the crosshairs of the Loup-Garou.

In book 5, Death Masks, John Marcone pops up again after being missing during Grave Peril and Summer Knight. Marcone has Miss Sigrun Gard at his beck and call as a bodyguard. Later, Marcone gains possession of the Shroud.

Does this strike anybody as the actions of a man who is introduced to the reality of magic in Storm Front? I think there's backstory on Marcone that we don't have yet, but he was already looking for a way to exploit magic for his own prestige and power.

Considering Jim has said a follow on series with Goodman Gray is in the offing, with Harry featuring as a frenemy, it seems unlikely that magic will go away. The Never Never, things that go bump in the night, vampires, wicked fae, all would seem to feature as prominently as they do in the Dresden Files.

Although Harry and the BAT might cause another change in the magical side effects of mortal magic. Harry might be able to get a cell phone! And drive a reliable car!

At the end of BG, Harry goes with Molly to the Carpenter's house for Sunday dinner. When Michael drops the bomb that he knows she's the Winter Lady, he then expands on the preparation they've done to get ready for Molly to come over. They've broken out her Grandmother's silverware.

In Fool Moon, Bob is explaining about different kinds of werewolves. Loup Garou are cursed to be consumed by a wild spirit. But it's not a run of the mill curse. You've got to be really powerful. A major sorcerer, a demon lord or a faerie queen. And, the only way to stop them is with inherited silver.

Do we know a faerie queen with inherited silver? Why, yes. Yes we do.

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

Michael is the ally that is now an enemy. Michael will be a Blampire or Rampire.

Mirror Harry works with Marcone.

Who was dead and is alive in the Mirrorverse. Clearly, this is Murphy.

One friend who is changed for the worse. Molly, who is either a warlock and on the run or is dead.

Someone he learns a great deal about will be Chandler. Jim dropped a big hint that we'll see Chandler again in the Mirrorverse.

Man, listening to the audio book of Battle Ground and different stuff is sticking out that I just zoomed past while reading.
Here's another. It really stuck out at me in the audio book, but I zoomed past it reading.

“We have to answer for this,” I said quietly. “We have to help. The wounded.” I didn’t look back at the dark opening in the base of the Bean. “The dead. We owe them. You know I’m right.”
“That could be a tough sell,” she said in quiet answer.
“I’m not asking,” I said. “My fealty is a two-way street. I have gone above and beyond my duty to Winter, right in front of God and everybody, by doing what no one else could. Now Winter will respond in kind, by helping as no one else can. You will help them. Every one of them. Do it in secret, no connections. We’ve interfered in their lives enough. This will happen.”
The Winter Lady gave me a very long, very intent stare.
And then she shivered and bowed her head.
“Already you have bound a Titan. And now a Queen. Sometimes,” Molly whispered, “I’m very proud to be your friend, Harry. And sometimes you frighten me.”
Sometimes I frightened the Winter Lady. I shook my head.

The fae CAN'T leave a debt unsettled. Just like Mab had to repay Waldo for removing the rebar from her neck, even if it is held against her as a favor, the debt has to be acknowledged and balanced.

When Harry said he went above and beyond his duties as the Winter Knight, he wasn't exaggerating. Harry Dresden couldn't bind a titan. The Winter Knight couldn't bind a titan. The Warden of Demonreach can and did.

Winter has no hold on the Warden of Demonreach.

Winter owes the Warden for binding Ethniu, in support of the accords, and Harry collected. Molly has no choice in paying for the injured and the dead. Just as she has no choice in collecting on the favor Harry owes her for making the glamour he used to evade Eb.

Which puts a different spin on Molly presenting the envelope to Harry on Christmas Eve at the Carpenters. She's not giving a gift, she's settling a debt. Which clearly underlines Harry as an unreliable narrator.

Which, in turn, expands on the unease Molly felt when she left the house in The Good People. She isn't human any longer, and she thinks Harry knows it. She thinks Harry is the same as she is because he so casually bound her with fae logic and Winter's debt to the Warden of Demonreach.