So i've already made a topic about it couple years ago, but in the light of some rewrites, additional information and all that, let's try to figure it out again. Also with this topic people won't need to reread previous one in it's entirety. With new information from 13.5 the rabbit hole goes deeper than ever. Overall the topic is intended as more of a collection of information and place of discussion rather than a definitive answer, so i welcome any corrections, extra points and theories. Now that we know for a fact that it's not only about time travel, but parallel worlds even moreso the actual game versions are canon this becomes a hole deeper than ever before.
Candidate #1: Maria/Marianette/whatever version of her
This is the basic boring theory that went around for as long as Madame X existed, but it got some merits for sure. There are a lot of things that work for it, but some critical things also work against it.
Why it can be her:
1) Her appearance. In the Ecclysia Pyramid we broke her mask and saw that she had black hair. It is the Archetype that gives all siblings golden hair colour, but natural hair colour of her mother, Anathea, is black as well, which lines up.
2) Strongest point for this theory comes In 13.5 where we learned that Nastasia entered Team Xen to "find her friend". and Ren was able to speak to said friend although this friend denied everything. This piece of new information heavily implies that Madame X is Maria and Nastasia knows it very well, as we know they were best friends. And implied "finding her friend" is something more akin to bringing old Maria back.
3) Melanie (a version of Melia) also called some "Father" for help and received a proper Yveltal nuke, similar to how Madame X uses Yveltal which implies connection between the two.
4) Madame X calls her "mother" in quotation marks, implying either that she wasnt biological or extreme disdain for her. Considering how Archetype children come to be it's fair to say she could consider Anathea not her real mother. And her mother dying to protect her would line up with Anathea dying in the mansion.
5) Madame X hates people being confined, which could be tied to Marianette and her living in mansion-prison.
Why it's unlikely to be her:
1) The whole bit about "Father, i have lost..." makes no sense in the context (it's sitll in 13.5, yes). If you assume mentioned father is Vitus, she has no reason to say that considering the relashionship of any Maria/Marianette version with Vitus was... pretty shit, and there are no other candidates really.
2) However if you think about Anathea as Maria/Marianette's mother, Madame X's extreme animocity towards her mother make no sense whatsoever. In all versions Anathea was shown to be nothing but loving and caring towards Maria/Marianette and was always on her side, and Maria/Marianette answered with love as well.
Candidate #2: Erinea
Erin as a theory only came to existense in v13, but had some strong arguments going for it. That said, like with #1, there are some extremely critical things that make no sense if Erin would actually be Madame X.
Why it can be her:
1) Once again appearance AND the point about mother. See #1.
2) In new 13.5 Darchlight sequence we have seen that Erin shows extreme physical prowess, well outside of what others are capable of. Is this limited to Darchlight cave or not is unknown, but Madame X is similarly extremely strong.
3) Strongest point for Erin being Madame X is, of course, infamousely repeated words of Erin in the flashback and Madame X in the prologue word for word. Which more or less created this theory to begin with.
4) It's more of a general observation but Madame X and Erin has the most similar way of interacting with other people, in mostly cold and smartass manner.
Why it's unlikely to be her:
1) Erin hates and despise Vitus, anything "Father" related makes no sense assuming she talks about him. No other candidates so far.
2) I'm fairly sure Erin isn't even aware how Anathea died since by this time she was in her prison with Allen and Alice, so her saying her "mother" died to protect her makes no sense.
3) Madame X spoke about Erin in third person. While it could be a calculated effort to conceal her identity, i don't think she would even bother.
Candidate #3: Nora Royer
This is the most interesting theory, but it also heavily relies on certain assumptions that were not really mentioned in game or explained yet.
Why it can be her:
1) This is the most direct case of Taelia dying to protect her in Where love lies, and "mother" being in quotation marks can be explained by her knowledge about Maiden of Reincarnation. This is also the only theory where "Father, i have lost..." make sense, considering she loved and respected Kenneth.
2) We never directly saw Nora die, only her getting encased in stone. Combined this with 2 times (it's not much, but weird that it happened twice) game mentioned her in important colour can only mean she holds some significance still.
3) This is a very "meta" argument but now that we know that every version is a new attempt to bring the entire thing closer to a "perfect ending" by either Karma or god knows what else, i want to point out that initially "Where love lies" was called "Version -1", in theory predating even beginning of Rejuvenation cycles on a meta timeline.
4) I will quote here a thing about Vitus, "Yveltal is how he spies, how he knows". Yveltal was present there when Taelia and Nora died, what significance did they hold for him at the time? Yveltal carried Soul stone on it in our Blacksteeple encounter, it is possible he took Nora's soul inside of it in WLL.
Why it's unlikely to be her:
1) Appearance doesn't really match with what we saw in Ecclysia Pyramid. In WLL little Nora had purple hair like her mother.
2) Nastasia and Nora lived in different times and while its certain Nastasia engaged in some time travel and Sheridan was close, it is unlikely they would become friends. Again this is only assuming "friend" she is talking about is Madame X.
Candidate #4: Garufan Inc. member
Okay this will be a more disjointed thing since this can only be told as a full story, but this is another can of worms 13.5 opens. In 13.5 Maman was HEAVILY rewritten and she told us about 2 stupidly importan pieces of lore which change a lot of things. From karma files we know that Garufans fought Arceus, 7 billion died and in the aftermath of Arceus destruction they started pretty much dissapearing and deteriorating, and that led to Variya making her project and Garufan civilization dropping below ground.
Maman told us that very slightly important thing that there is fully functioning Garufan tribe just chilling somewhere underground and this is where she came from. It's been no more than 10 years since she came above ground based on circumstantial things, so in that short timespan this Garufan tribe couldn't die out, they are just chilling somewhere underground. Second extremely important thing is the "Light plague", an illness that killed Maman and killing Franchesca. Any garufan that is subjected to above ground will immediately develop "Light plague" which inevitably will start killing the host, and i think it's fairly obvious that this is what started killing Garufans after the whole Arceus shebang.
Now i'm willing to remind you that a bit under Sheridan we can find a machine that makes a copy of Madame X armor, so with this new piece of knowledge it's a plausible theory that Madame X was a garufan woman, and this armor was constructed to counteract the "Light plague". It's highly unlikely she is Variya, so it doesn't help us much, but this connects some dots for sure.
Candidate #5: First Human/Queen of Aevium
While before there were heavy implications that Vitus and Nymiera were first humans from legend about Arceus, we also learned that Nymiera and Vitus are pretty much constructs. Correct me if i'm wrong but i also remember hearing in Zeight that a lot of stuff predated Nymiera, which also throws her age off. In the legend pokemon became weaker, and humans received supernatural strenght and agility. As a sign of humiliation first male also gifted first woman his sword, and Madame X seems to favor the sword quite a lot. However in this case any "mother" and "father" mentions are kinda moot, even if you consider Arceus a mother or a father.
Another thing that was slightly retconned is that now there was a Queen that ruled all 7 kingdoms of Aevium at some point. Which i'm gonna throw out as a possibility here.
Some interesting points i'm not sure where to leave:
Madame X warned Kanon about Theolia monthes before the thing happened. This still confuses me.
Madame X hates to see people confined.
Madame X said to Melanie "no more hiding behind that beast" about Yveltal which can be just a random remark but seemed quite... rude i suppose to kind of eyes of Vitus.
This is not a definitive statement, it's an opener, so feel free to add, discuss and present other theories. Most incredibly flaky ones like Madame X being Nastasia, Amber, or Anathea are extremely unlikely so i didn't even bother. I will also try to add important points if they arise.