It is no coincidence that Stannis will be leading the Battle of Ice while Daenerys and co fight the Battle of Fire. Both events will be important milestones in lead each character to their impending destinies.
Stannis is trying to navigate and survive a wintery world. If successful, he will have a significant headstart over competitors. Additionally, he may learn more about the ancient magical forces that operate in the North and at the Wall especially.
The plot seems to be heading in the direction in which the red priests of the Free Cities will fully align themselves with Daenerys. This factor reduces the chances that they will experience a wholesale disillusionment with her level of adherence to their expectations for Azor Ahai.
It is frequent that individuals purported to be messiahs gain the ability to set and decide doctrines and courses of action. This often creates a split between supporters of the putative messiah and groups that reject the new movement as being too heterodox (often clerical institutions do this). The perceived messiah, if successful, frequently ends up creating a new amalgamation with striking differences from the original sect (or maintains the sect while recasting its teachings).
Another factor is charismatic authority. In Daenerys's case, the anti-slavery crusade will create such a frenzy and expectations of hope that her degree of conforming rigidly to preexisting plans will not dash the support of the red priests for her. Probably after her looming conflict in the Dothraki Sea, the same will mostly happen with the Khals.
Benerro, Moqorro, and the like, barring glamors or some yet unrevealed hidden agenda, are too invested in supporting Daenerys as Azor Ahai to let differences of opinion on some matters derail the alliance. They likely will accept being a component, albeit, a significant one, in her coalition. Given that they have portrayed her as R'hllor's chief earthly instrument for inaugurating a new golden age, they are bound to accept her decisions within broad parameters. If they are convinced she is the geniune embodiment of Azor Ahai, her overall mission cannot be heretical, even if not all of her views perfectly align with the present ideas.
The collective view of Daenerys's coalition will lean more toward a political objective than a religious one, though both will exist simultaneously.
There is an enormous amount of foreshadowing suggesting that Daenerys is Azor Ahai and that the dragons are Lightbringer. Jon's discussion of some text found in the Jade Compendium is but one of many examples pointing toward heavy parallels between the dragons and the original AA's weapon. There must be some reason that Martin had Aemon give Jon the Jade Compendium and then proceed to comment on those specific passages. The House of the Undying visions and the events at the pyre which gave rise to the dragons are also amongst the list of reasons to connect Daenerys to AA and the dragons to Lightbringer. The history suggets that the Lightbringers are fire based and connected somehow to Asshai (from whence the first dragons originated).
However, there might also be a duo or trio of heros, depending on the meaning of the PTWP and the "three heads of the dragon."
I'd say that, like Benerro, Moqorro truly believes that Daenerys is Azor Ahai and is bent on helping what he perceives to be her mission. Helping Victarion acquire control over the horn presents risk to Daenerys, but it may be that it is the best/least bad arrangement from Moqorro's point of view. Euron is presently believed to be its master. Both Moqorro and Victarion consider Euron a mutual threat. Furthermore, Victarion has shown signs of being a useful tool for Daenerys, more of a help than a hindrance, as she could use the Iron Fleet's services. Moqorro may believe this kraken is likely enough to prove to be a servant of R'hllor and Daenerys to be worthy of mastering the horn.
In many ways, Melisandre seems more secretive and suspicious in her agenda regarding Stannis.
As things stand now, it looks like an acquittal is highly probable. The present state of the case is such that a jury would not believe the accusations. However, there are three primary sources of threat for tampering with this trial: Varys, the Sand Snakes (Especially Tyene; maybe Nymeria), and Qyburn. All three are quite possibly willing to go to any lengths to achieve their objectives, though even they would be hard-pressed to pull off causing a guilty verdict. Still, it is in the realm of probability that they could fabricate a scenario which makes Margaery appear suspicious.
The trial is going to have some kind of jury. It is unclear exactly what its makeup may be, but the conversations involving the HS make it sound like it could be an all female jury, with three individuals representing the three feminine aspects of the Seven (excluding the Stranger). If true, this would mean someone to reflect the Mother, someone for the Crone, and someone for the Maiden.
Basically, if any sign emerges that Tyene is one of the participants, that is very bad for Margaery.
I would say that the Westeros's present situation is unusually propitious for some level of challenge to the power of the nobility to emerge. Of course, the aristocracy will not disappear and there are limits to how much diminishment it can experience by the end of the series, yet several factors are in favor of alternate social forces acquiring power at its expense.
One sign of this is that the suppression efforts against the BWB have been going quite poorly. This is in part due to hatred of the BWB's opponents, however, there are other reasons as well.
Another case is found in the present potential of the Faith Militant versus its past record.
In the past, at least during the reign of the Targaryens, religious resistance to political power faced far more a unified and determined political system. This was the case during the Faith Militant uprisings which occurred during that dynasty's rule. There resultantly was less incentive for nobles of various levels of power to risk associating with it. However, now the scene is much more fragmented and the space for stirring up a climate of hysteria is massively increasing. Given that this is a premodern society, aspiring kings and noble elites have much to gain by hammering away at opponents on the theme of being true believers vs fighting faithless opponents. Thus, the wave of religious revivalism has a strong potential to keep gaining momentum. The longer that the High Septon and the sparrows can keep building up their networks without heavy resistance, the more likely it is that political powers will be forced to work with, rather than against, them. Confirmations of necromancy and the like will only exacerbate the desire to setup an inquisition-like approach to eradicating such forces.
It is a technique that is used repeatedly in basically all political systems under a variety of guises but is particularly effective when it is centered around an enormously powerful force like religion.
There are some things about the Iron Bank's support that increase the probability that Stannis will gain the throne some point. One is that it obviously makes his cause more powerful, as Jon observed. Another interesting thing is that (TWOW sample chapter)
Not surprising that a few more will take the throne before the end. It is basically a necessity to the plot for the throne to fall out of Lannister hands in TWOW. Aegon is a prime candidate to hold it at one point, given the second Dance of Dragons. There also are various instances of foreshadowing that Stannis may gain it as some point, as in that vision mentioned in ASOS and in a TWOW sample chapter