2 restricted cards catch my attention first. I would remove
Things in the Ground (SoA) even that is amazing mill card also. I feel Negotium is essential for mill&stall decks. I am not fan of
Curse of the Stone (TWB). It works good with
The Large Man (TSS) but it doesn't make your board position any stronger and it is bit too slow. I think
Blackmoor Estate (Core) is the best mill card. It is permanent and you can use end of opponent turn. Mill decks needs better cards just for stalling. I would think adding small Miskatonic support to get
Museum Curator (TWB) and card draw. Then I would add couple
Dimensional Rift (SoA). Also Calling Down the Ancients and A Single Glimpse are not so good when playing with Negotium because opponent will just sacrifice small skill characters which are not threat for you anyway when you have Negotium in table. I would like to see some support faction with about 10 cards in this deck. 2-3x Black dog from new set and 6 other Shub cards would work also But I haven't tried Mill decks yet thought so don't have so much experience. Drop by for some games in Helsinki.

Damn, didnt notice Negotium is banned also. That will seriously mess with the strategy here, as the point of the deck was to sit behind Negotium, get Yog out as fast as possible and blast away repeated Curse Of The Stones to win. Usually 2-3 is enough if there's Things In The Ground in play. But yeah, if i have to choose between Negotiation or Things, the Things will go.....
I'm not a huge fan of Blackmoore Estate. I had it in an earlier version of the deck and it seemed to drain away my resources too much and get blown up too quick. But, it is pretty much my only choice now.....

I'd try adding other ways of milling cards, e.g. Terrors in the Dark (SoA) or Ritual of Bellephar (IT). I'm also partial toThose Without Faces (TSotS) but their effective use probably requires a different kind of deck.

If you are adding a second faction, Hastur's got Cold Spring Glen (DD) and several additional (but less effective) characters and support cards that have milling effects. It has also several cards that allow you to stall the game a bit, e.g. The Seventy Steps (IMoD) and The Cavern of Flame (ItDoN).

Terrors In The Dark is already in there 3x. Definitely one of the better mill cards. Ritual Of Bellephar on the other hand is a bit problematic. It almost got in on this version of the deck, but was cut due to the strong synergy between Things In The Ground and Curse Of The Stone. But now that i have to change the theme of the deck due to new restricted list, it might make it in this time.
Main problem with milling strategy in my opinion is that if you just base your deck on bunch of strong milling effects, it won't be fast and consistent enough to maintain both strong milling and board presence. That's why milling has to be done with a simple and efficient combo that can empty opponents deck extremely fast, while leaving majority of the deck for maintining enough of a board presence to keep opponent away from stories.

The original intent of this deck was to trick yog-sothoth into play as fast as possible, fill the board with insane characters with TitG and finish with repeated massive curses of the stone. The original form of this deck was very hard to beat when it got going, but unfortunately that was very rare. The addition of negotium was supposed to help with the consistency problem, but alas, it wasn't meant to be.....

So, should i add another faction in the deck? The ones mentioned, Academy, Shub and Hastur, all are in their own ways viable. Academy would add speed and consistency with Museum Curators and card draw, but due much weaker characters compared to Yog, it would make the board presence of the deck weaker. Hastur has the same problem and i have never been a fan of milling cards in that faction. Shub on the other hand could increase the speed of the deck without losing board presence, but to really get enough kick out of Shub cards, i would propably have to limit the amount of milling cards, which would be devastating for the deck without some combo as a win condition.

Currently the following cards are going to get cut out, but dunno what the replacements are going to be:
3xTitG
1-3x Yog
1xLarge Man
Sac. Cards

I think one problem with milling decks is that players put just too many milling effects to their decks. Number one priority of the milling decks should be stalling the game and denying story wins for opponent. That is why every milling deck should have 3x
The Red-Gloved Man (WitD) and 3x
Negotium Perambulans in Tenebris (DD) always. Problem with one shot cards used for milling it is that it makes you bit closer to winning but doesn't stall game at all. You never want to draw Mill card like
Ritual of Bellephar (IT) when you are in bad situation. In good situation you are already doing good and that card might just become "win more card". That is why permanent milling cards are so good. You can always use
Blackmoor Estate (Core) at end of opponents turn if opponent didn't put any new threats in play. I would recommend Hastur also for second faction.

Cold Spring Glen (DD) is very good. Then you can include
Stygian Eye (IT) and
Infernal Obsession (TAD) to deal with bigger threats.

Also some sort of small Shub package might be good like 2x
Snow Graves (AtMoM) 2x
Shocking Transformation (Core) and 2x Black Dog from the newest set. So many options

That's definitely true for one-shot effects. They just end up being win-more cards unless used in a right situation, which is rare. Both Stygian Eye and Black Dog would be awesome choices for the deck, but they are both already in my freaky shub/hastur control/insanity deck, and as i don't have a printer proxying would be difficult and annoying, so going to stay away from those cards as much as possible. Cthulhu would also be tempting with all the destruction cards to eliminate any characters i can't keep stalled, but kind of annoyed with cthulhu because of all the Khopesh nonsense (though i have to admit i also have a Khopesh deck.... xD). Ravager would have also been awesome for stalling.

Too bad Cursed Skull combo is far too unwieldy and doesn't synergise well with Negotium, as i really love that combo. (Cycle Cursed Skull with M.U. Museum Of Natural History for repeated sacs.)