In the interests of focus, I analyzed the domino clues only, and offer here a short list of questions that feel more likely to be comprehensive on this subtopic than the sixteen questions I posted before.
The first bit of analysis (or "data reduction") on the sprawling set of clues we have was to consider how many independent points of information we have concerning the dominoes. In all, we have seen dominoes over a dozen times, if you count out-of-story references (like the cover of issue #2), but it seemed to me that these can likely be clustered into four. Then we can consider separately how the possible answers to those questions align with the facts and with each other.
The four elementary domino appearances in the story, in my formulation are:
D1) El Penitente alluded to a force acting on his behalf as "The Mexican Train". We know this to be the name of a domino game.
D2) The dominoes that have appeared in Gotham on three occasions when someone likely to be working for El Penitente was defeated in some way.
D3) The dominoes said to have been found in cases where the Black Glove members from #680-681 were killed or abducted.
D4) The dominoes Pearly was playing with when Batman spoke with him.
And furthermore, let's throw out a list of the likely suspects:
S1) El Penitente or his agents
S2) The Joker
S3a) Out to get El Penitente
S3b) Framing Damian
S4) Bruce Wayne from the past leaving dominoes
S5) Grant Morrison
S6) Oberon Sexton if he is not one of the above
S7) Two of the above taking turns
Finally, here is a timeline of events relevant to the Domino plot. I give an approximate count of the days since the end of RIP. There is a big jump from RIP to the "six months later" when Dick and Damian collar Le Bossu. The smaller scale of the timeline (eg, events shown in Batman and Robin) are in order (although the actual day of Cardinal Maggi's death cannot be pinned down). The absolute count of days is guesswork, and probably not important.
T1) RIP+000 Malenkov killed by the Joker
T2) RIP+001 Jezebel's plane attacked by Talia's man-bats
T3) RIP+178 Drug deal with dominoes in the trunk
T4) RIP+179 Toad dies, domino in hand
T5) RIP+180 Domino in Pyg's lab
T6) RIP+181 Cardinal Maggi slayed
T7) RIP+185 Santo
Oberon Sexton arrives in Gotham: RIP+183
El Penitente and Sexton phone call #1: RIP+188
Pearly and Batman: RIP+190
Oberon Sexton and Batman: RIP+200
El Penitente and Sexton phone call #2: RIP+200
al-Khidr DEAD <183, Sir Anthony MISSING/DEAD <183, Malenkov found <183
Given these facts, the three primary questions concern the cause-and-effect relationships (or lack thereof) between the "D" items. For the sake of brevity, "EP" = El Penitente.
1) What is the relationship between EP's "Mexican Train" and the dominoes in Gotham?
1A) EP is using dominoes as a symbol
1B) EP is using dominoes as a weapon
1C) Someone opposed to EP is using dominoes as a reply/taunt/clue to EP
1D) Gotham dominoes to frame Damian
2) What is the relationship between the dominoes in Gotham and Sexton's report to Batman?
2A) Dominoes with dead BG members same agenda as ones in Gotham
2B) Someone is using BG dominoes as a copy of Gotham ones
2C) Someone is using Gotham dominoes as a copy of BG dominoes
2D) Sexton's story is made-up to link to Gotham dominoes
3) What is the relationship between EP's "Mexican Train" and Pearly's dominoes?
3A) Pearly knows something and was trying to tell Batman nonverbally
3B) Pearly has dominoes because he is a defeated criminal
3C) Pearly has dominoes as part of a plan to spread them to many people
3D) It is a coincidence that Pearly has dominoes
Phosphorus Rex says El Penitente's forces (or those of Pyg, who works for El Penitente) will "kill us all".
The secret of the dominoes is "terrifying".
While everyone seen in Gotham with dominoes is an underling of EP who has just been defeated when the domino is found, the Circus of the Strange are underlings of EP and are defeated and do not end up with dominoes.
Grant Morrison interview: "this isn't about Bruce Wayne at all, except in as much as it deals with his absence".
The one BG member whom Talia took out was not found with domino.
The one BG member whom Joker killed was found with domino pattern. But if the dominoes
are "terrifying", then the symbol may be an imitation (or fiction) by a copycat who failed to understand the significance of the physical dominoes.
The solicit for #1 said that Batman and Robin would be tracking the Domino Killer, who had abducted a child. Sasha was abducted by Pyg. So either the Domino Killer is on El Penitente's side, or Dick would have been making a mistake in his detective work, or the story was changed significantly after that solicit was written.
Solicit for #12 says that the Domino Killer's identity will be revealed (but there strong indications of misdirection; e.g., that there is no Domino Killer).
Was Malenkov's body taken from Gotham and put into alligator elsewhere? Either someone took great trouble to create an impression or Sexton is lying
Grant Morrison interview: re: the Joker, "an idea I don't think has been done before with him".
If you compare the art between Batman and Robin #3 and Batman #676, it looks like Le Bossu was in the "House of Hurt" where we first saw the Club of Villains. The newspaper announcing Cardinal Maggi's death was there, and the policeman had been inquisitive about something, perhaps tracking the Black Glove murders to Le Bossu and thus to Hurt / El Penitente.
I don't think it's possible given what we know to pin down the answers to the Domino questions, the identity of the Domino Killer, and the identity of Oberon Sexton. That said, I think some answers look more likely than others. If the secret of the dominoes is "terrifying", then they are not a message from Bruce Wayne, and they are not a mere symbol or hint-for-hint's sake, like Jason Todd's calling cards. Talia is unlikely to be leaving the Dominoes, because Jezebel was not found. If she were merely using them to frame Damian, that would not be terrifying.
I have argued for a Fourth Wall scenario in which Grant Morrison was the Domino Killer and/or Oberon Sexton. This remains possible, but we are now very close to the climax of this plot without much commitment to that outcome, and a lot of story left to tell regarding the main characters.
Perhaps Pearly's role is of lesser importance, but I think he knows about the dominoes and used them (instead of a drawing on paper) to tell Dick not only where the Lazarus Pit was but also that the "Mexican Train", Doctor Hurt's big attack, was coming. Note that the guard makes at least two references to Pearly being too talkative, and Pearly chooses to communicate his key point to Batman silently.
As I noted in a previous post, I think Sir Anthony makes a lot of sense as Oberon Sexton, but this is far from conclusive. Sexton could also be Mangrove Pierce, as I conjectured much earlier.
And so, I think the Domino Killer is most likely either El Penitente or the Joker. I think the single strongest interpretation of what we know is 1B, 2D, 3A, as presented in Theory #1 below. However, as a demonstration that the mystery is not, as far as I can see, solvable, I offer two other theories which also fit the facts and are not, as far as I can see, falsifiable. In fact, Theory #1 fails to do anything original with the Joker, so for it to be true, the plot will have to conclude with the original idea for the Joker coming in later.
Doctor Hurt is going to use drug/toxin on dominoes to cause a mass slaughter. The dominoes are also being used as a suicide/punishment to kill his underlings when they fail. The Black Glove murders, committed by Joker and Talia, are not actually being marked with dominoes; Oberon Sexton (Sir Anthony) made this up to get Batman's help.
The Joker is doing the Domino killings and leaving dominoes in other places, just to vex Doctor Hurt. He knows about the "Mexican Train" and has chosen to use dominoes as a taunt. "Tony Li" was a Joker henchman in disguise who planted the one on Santo. Oberon Sexton is Sir Anthony, trying to get Batman to stop the killer who might be after him next.
Doctor Hurt is going to use drug/toxin on dominoes to cause a mass slaughter. The dominoes are also being used as a suicide/punishment to kill his underlings when they fail, or as a symbol of his work, and this includes the Black Glove members. Oberon Sexton is an amnesiac Joker trying to be a detective and work for the good against evil, in the guise of a voodoo loa Baron Samedi.
Other permutations are possible. The point is that we can, I suspect, narrow the possibilities down, and see as we read which choices Morrison made from a list of known alternatives. Even so, there are sure to be utterly unforeseeable twists, not to mention the truth about Doctor Hurt, the Wayne family, the return of Bruce Wayne, Talia's attack on Dick Grayson, and whatever makes this part of the story tie into Batman #666 "considerably".
Whatever the truth is, we now have a yearlong plot coming down to the final two issues, with the penultimate installment out tomorrow. And as the preview for #11 shows, it's a big one. The showdown: Doctor Hurt versus Dick Grayson. The action starts now!