Why not ALL of both? Show me one source that states the two are mutually exclusive? The only evidence for this notion is the assertions of a military officer & glorified bodyguard that in HIS comparative analysis of an immense work of obscure prophecy, one version is corrupted. The example he cites is that the wetlander prophecies do not mention Rand kneeling before the Empress. Well, nowhere does he even suggest that the prophecies say he will NOT kneel, so they are NOT mutually exclusive! Nowhere does anyone, including RJ, so far as I know, claim that the Karaethon Cycle includes EVERY prophecy ever made concerning Rand or that it mentions EVERY detail of his career as the Dragon. Just because an event that takes place is not in the Prophecies does not prove that they are wrong or flawed or corrupted or amputated. Not only that, things happen in the Prophecies that better scholars than a Seanchan military officer misunderstand all the time. Min cites the prophecy she and Cadsuane think refers to Callandor which it appears that the conventional wisdom believes refers to a political reorganization! Moiraine says early on that there are no references to the Aiel in the Prophecies of the Dragon, and yet, one of the very first Prophecies that we hear in EotW is a reference to the Aiel, when in Baerlon Thom tells Rand the following: "the Stone of Tear will never fall until the People of the Dragon come to the Stone." This particular prediction appears to be such common knowledge, that even a shabby gatekeeper at an inn in a backwater town at the ass-end of nowhere grasps the significance of Logain calling his followers "People of the Dragon" and does not feel any need to elaborate on that tidbit of news. So how do you explain Moiraine's claim that there is no mention of the Aiel in the Prophecies? Another epic mistake on her part is her claim that the prophecies do not mention Mat or Perrin, and yet we get two separate verses in KoD, both mentioning Mat & one mentioning Perrin!

In both cases, and very likely in the case of the "differences" between the two versions of the Prophecies, the explanation is that the character claiming the Prophecies do not mention things is unaware of the references to those actual things. How is Moiraine supposed to recognize the verse Noal recites as obviously refering to Mat? Did even we, the brilliant readers note at the time that it might very well have been a reference to Tuon herself? "Fortune rides..." seems a lot more meaningful now that the Daughter of the Nine Moons has taken a higher name.

So as far as the discrepancies between the prophecies, there are one of two immediate explanations:
1. The things that are supposedly omitted are, in fact, not. Rather they are phrased in a way that makes people who are unfamiliar with the details of the event or persons mentioned miss the reference or its meaning. Thus Moiraine overlooks the mention of the Aiel in an extremely well-known prophecy and a Seanchan dilettante could completely miss a reference to the Crystal Throne or the Empress in a prophecy written or spoken by someone who had never seen or heard of either one. Maybe the prophecier had an image-type vision of Rand kneeling before a glowing throne and mistook it for the Creator's throne or something, or simply called it by a name that would not connect with the office or person of the Empress in the mind of a Seanchan.
2. Even if there is no reference to an event in one prophecy, it does not mean the other prophecy is wrong to mention it, nor is it proof of contradiction between prophecies, unless one prophecy is completely in opposition to the other. If one says "he will never kneel before the Crystal Throne" and the other says "he will kneel before the Crystal Throne" THAT is a contradiction. And even if there are contradictions, they could be simply false interpretations. For example, one version could say "He shall never kneel before the Crystal Throne" and another could say "He shall kneel to the child of the hammer and offer justice to her." Maybe a Seanchan would not get the latter reference and would take the former to mean he will never kneel to the Empress, because in the Seanchan mind, the two are linked, just as in the USA we refer to the President and the Oval Office as one and the same. Meanwhile, it could mean something as literal as the fact that when Rand does kneel to Tuon, she is on this side of the Aryth Ocean and not in possession of the actual throne itself. Perhaps the Seanchan reader might not know that Hawkwing was called the Hammer of the Light in the wetlands and completely miss the reference to her in my hypothetical prophecy. And who can say what it means by justice? Will Rand submit to her judgment or will he offer to pay reparations for the harm he has done her people, or will he simply offer his new-found sword as part of the ritual of submission, with no one actually realizing that the sword in question is (supposedly at least) Hawkwing's own Justice?

That's a fun little bit of fan fiction, but where is the evidence, aside from your own extrapolation with Ishamael's character? Given especially the theme from the very beginning of the series about how things change over the passage of time, this seems like an absurdly long gambit to play. The supposed back-story I have seen offered for these machinations suggests that he is able to predict the ripple effect on a culture ten centuries in the future that will result from his altering a few phrases in a prophecy!

Occam's Razor suggests that the devotion to the Empress, both in her person and office, is the natural result of a deliberate campaign or else an organic understanding that the rule of the Empress IS the glue holding together this enormous, continent-spanning Empire, cobbled together from widely varied regions, cultures and ethnicities. There are so many centrifugal forces in any multinational empire or multi-ethnic state that they NEED something that can bind them all together. That is generally, in the case of successful empires or confederations that manage to hold off their dissolution, a common ruler or other common focus for the loyalty of otherwise disparate peoples, particularly under such a pervasive bureaucracy and brutal enforcement of Imperial rule. While you can rule to a certain extent with fear, you also need to offer something, even if only symbolic, to get people to go along. They need an excuse to believe and to convince themselves that they are not being cowed into submission, they are adhering to their love of the (blank). Even the highly repressive Stalinist USSR, during World War Two, began recalling all sorts of nationalist institutions and symbols they themselves had banned and savagely driven from the public eye, such as the church and patriotic or historical symbols.
The above phenomenon is a much more likely explanation for the reverence given the ruler of the Seanchan Empire, than some clever rephrasing of the Prophecies a thousand years ago. That would be like suggesting that people want to ban flag-burning and make the Pledge of Allegiance mandatory, because someone altered the Bible early in the eleventh century. Such a theory would be ridiculous, and the Bible had a far greater impact on American culture and political development than the Karaethon Cycle has in the world of WoT. That is simply a prophecy of the end times - the WoT equivalent of the Book of the Apocalypse, without all the rest of the Bible, such as the Psalms or the Ten Commandments or the Creation story and the fall of Adam and the Gospels including the Sermon on the Mount and the Passion, and the Epistles of Paul and all the rest. Really, Apocalypse is one of the least influential books of the Bible, despite the glamor of the end of the world stuff, and one of the least understood or known(for instance, everyone gets the Four Horsemen wrong). The Karaethon cycle AT BEST holds an equivalent place in wetlander or Seanchan culture to the Book of Apocalypse in ours. And let's not even get into the fact that the people who run the media don't even acknowledge that book as divine Scripture (which would probably explain everyone getting the Four Horsemen wrong). To assert that a particular cultural trait, which follows a principle often seen at work elsewhere in the course of WoT (i.e. Rand's followers all preferring him to their erstwhile allies, and only keeping from fighting one another by their obedience to him; various mentions about how people are trained, etc), is the result of a subtle manipulation of a writing that holds little or no direct importance to anyone who dies before the events foretold therein come to pass, is a bit too over-complicating for me to accept.

But isn't the whole point of Egwene's storyline to put her in a position to stop that shit?