There has been an intense amount of speculation concerning the nature the Merovingian and the statement by the Architect concerning the “mother” of the matrix. I’ll tackle both of these issues in this post as well as appending a few comments on whether either the Architect or the Oracle lies to Neo.
The Merovingian is not the avatar of a former “One” – he (or it) is a program. Yet he is a program that can generate other programs and indeed has a great deal of skill in doing so… and in particular a great deal of skill in generating programs that produce specific sensory impressions for human subjects (i.e., the cake scene). What is the purpose of a program like the Merovingian? Obviously such a program would be of immense value in creating the matrix. And yet the Merovingian appears to have – despite his veneer of sophistication – very little appreciation of the psychological depth of his human subjects: he treats them as simple sensory organisms. This view of humans quite ironically mirrors his own lack of depth. He is very intelligent only in the sense that he has very specific skills; but he lacks the depth to appreciate anything beyond his particular skills and he certainly lacks the ability to empathize with other forms of intelligence beyond a very crude “we all want power” point of view.
The Merovingian was the original helpmeet who aided the Architect in creating the first two matrices that failed: the original paradise failure and the second, “historical” failure. As the Oracle noted when feeding the crows (?!? if this is not an ominous sign advertising her ambivalent, doom-saying role I don’t know what is…), someone had to write programs to govern the workings of the matrix… and the Merovingian would seem a likely candidate for devising the programs governing the machine/human-sensory-organ interface. Initially the Architect and Merovingian succeeded in creating an environment that satisfied all the physical, sensual needs of the humans, but failed – colossally – in addressing psychological needs. The subsequent attempt to incorporate the “grotesqueries of human nature” also failed, again due to the inability to properly integrate human psychology. Hence the Merovingian was discarded but was not, for whatever reason, deleted.
The fact that the Merovingian was an “extra-matrix” program (he operated on the matrix, not necessarily in the matrix) meant he had access to the back doors enabling him to evade agents and, more importantly, survive subsequent reloads. Plus, we have to recall that he retrieved a number of other programs and set them up as his entourage and/or bodyguards. This may well explain the origin of Persephone, whose name suggests that she was in some manner “seduced” by the Merovingian. (By the way, while we are touching on names, the significance of “Merovingian” would seem to be quite obvious – like the Merovingian kings of old, his position of authority was usurped, leaving him a mere ornamental figurehead in the actual workings of the matrix.) Persephone fell under his sway when he was an integral part of the matrix, when he had purpose. His subsequent fall, and his acceptance of a purposeless existence, is the basis of Persephone’s lament when comparing him to Neo. Neo has a purpose and it is in part this sense of purpose that draws Persephone to him and leads her to remark that the Merovingian was once like Neo. (This is not the first time we encounter this theme: recall that it was the theft of his “purpose” that drives former Agent Smith in his vendetta against Neo.)
So who rendered the Merovingian obsolete? It seems quite clear that it was the Oracle – with her understanding of human psychology – who replaced the Merovingian in the hierarchy of matrix programs. And judging from the antagonism he evinces, the Merovingian has never forgotten or forgiven her for this, for “stealing” his purpose. This is one very important reason why the Oracle is guarded by Seraph. It also goes a good distance towards explaining his implacable opposition to the successful working (via reloads) of the “Oracle’s matrix,” because the continued success of “her matrix” confirms the legitimacy of her “usurpation” (and his consequent purposelessness). I have also read that this antagonism has been used to explain the substitution of a new actress for the Oracle (at least in the video game Enter the Matrix), the old “shell program” of the Oracle having been betrayed to the Merovingian, who destroyed it.
There seems to be a resistance on some people’s part to accepting that the Oracle is the “mother” of the current matrix. I’m not sure where this springs from – the desire to avoid considering the Oracle as one of the “bad guys” or simply a misunderstanding of the Architect’s response to Neo when he mentions the Oracle – the Architect says “please,” which I took to connote exasperation at being (again) interrupted and at the overly deferential, indeed blasphemous, designation that humans have accorded her. The name “oracle” as a sign of human appreciation must have been particularly galling for he Architect, who quite clearly views the Oracle as an inferior, and yet he is still willing to acknowledge her role as “mother” – albeit with the caveat that she is “a lesser mind, or perhaps a mind less bound by the parameters of perfection.” (It seems quite clear that the only program with the requisite psychological, “intuitive” (i.e., non-mathematical) insight to function as “mother” as described by the Architect is the Oracle and I am frankly baffled by suggestions that the petulant, destructively manipulative Persephone could be in any way be considered the “mother” of the matrix.)
The Oracle’s insight into human psychology is what enables her to aid the Architect in constructing a matrix that not only works but also incorporates the flaws that are unavoidably introduced by the human subjects into a mechanism for reloading the system. In this regard both the Oracle and the Architect are on the “same side” – they both believe the matrix is the best solution given the situation with which machines are faced. And yet the Oracle and the Architect do not perceive the situation in precisely the same way. The Architect, although having made his decision, is unable to see past certain consequences. In this respect the Architect is in much the same situation as Neo, when he asks why he cannot see whether Trinity dies in his dream. The answer the Oracle provides applies to Neo and the Architect both: each has made his decision but neither can see past a decision he does not understand.
Although both the Oracle and the Architect are machines the Oracle has a deeper understanding of how this iteration of the matrix plays out, despite the Architect’s superior mathematical ability. The Architect and the Oracle have both made the same decision – they did so when they created the current (six iteration long) matrix, but the Oracle’s understanding of human psychology enables her to see past the current iteration. She sees that Neo will bring change whereas the Architect’s limited understanding of humanity only permits him to envision mutual destruction. So both tell Neo the truth regarding the consequences of his choice – at least as far as each understands it. The Architect and the Oracle, while not opposed to each other, do foresee different consequences stemming from Neo’s decision to save Trinity. The Oracle can foresee that somehow Neo triggers a reconciliation of sorts between man and machine that allows both to transcend the matrix as currently constructed. It is as an allusion to this otherwise unforeseen future that the Oracle’s comment that Neo has “made a believer” out of her assumes it full importance. (This does not imply that the Oracle “orchestrated” the love affair between Neo and Trinity, as has been suggested elsewhere – only that she foresaw such an affair as an inevitable statistical result and had noted the strong possibility that love would strike in this particular case.)
How this reconciliation occurs – and what role is played in it by former Agent Smith – is what we will presumably find out in the matrix revolutions. (Note the use of the plural – revolutions – one each for humans and machines…)
4:07:38 AM 
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