In my time here, I've seen several complaints about the "Imperialized," "hippie" (that is, Kynareth-worshiping) Greybeards in Skyrim. While there aren't many who are absolutely horrified by their presentation, there are plenty of people who consider their portrayal in Skyrim to be another aspect of the cultural homogenization that is also evident in the almost-total absence of the traditional Nordic pantheon (as we knew it prior to Skyrim) in favor of temples worshiping Imperial gods--which was, to some extent, necessary when building a game revolving around a traditional Nordic villain who was considered by old lore to simply be a different face of the same character that saved your bacon in the previous game, someone you almost certainly would not want to oppose. While the absence of the traditional pantheon in other walks of life is somewhat acceptable (considering the possible recruitment drive that the Imperial Cult might have indulged in after their chief god saved the world from Mehrunes Dagon), the absence of Kyne from Greybeard dialogue (despite her presence in the emblems on the road to High Hrothgar) is much harder to explain. These are, after all, the most traditional group of men that Skyrim as a nation and a province has to offer--or at least, so we've been told repeatedly (by sources that are no older than the Tiber Wars, for the most part--the PGE 1E and the Heresy both tell us that the Greybeards were important in those days, but we have no source from earlier than that that names the Greybeards specifically except for the origin story of the Ebonheart Pact in TESO). Their apparent adherence to Imperial worship therefore understandably rubs some folks the wrong way.
At the same time, a few people--not nearly as many as those who have complained about the Greybeards--have wondered about the absence of the Imperial College of the Voice in Markarth, as described briefly in the PGE 1E. The PGE itself laid the foundation for the Imperial College's absence, in the commentary by YR: "Septim's new college is staffed by hacks and charlatans--the so-called Grand Master is said to have formerly earned his living as a street performer in Windhelm--the students are scions of the most obsequious Nord families, hoping to curry favor with Tiber Septim's New Order." The statement states outright that the College has no foundation, and as such will probably not last long. The fact that no one in Markarth ever mentions the College is curious, but not really important or mysterious. That said, some of us cannot help but wonder sometimes about what happened to it.
It so happened not too long ago that I visited High Hrothgar and shook my head at the Imperialized Greybeards and happened to wonder how the game would have differentiated between them and the Imperial College if they had included it at all. The following theory almost immediately came into my head:
Septim might well have started the College as a means to undermine the respect and authority of the Greybeards by giving possible Thu'um students a different, Imperialized school in which to learn. Regardless of whether or not serious Thu'um students actually did choose the College over the opportunity to learn from the Greybeards, the fact remains that the College advocated the use of Shouts as a weapon of war once again. The Greybeards, and Paarthurnax, would be displeased to find this opinion being spread about in Skyrim once again. Is it possible, therefore, that the Greybeards and Paarthurnax found a way to drag all of the College's "teachers" to High Hrothgar and indoctrinated them with the Way of the Voice, making them Greybeards themselves? The College would, of course, disappear without its teachers, and the Greybeards would suddenly include a group of Imperials (or at least Imperial sympathizers) who would naturally worship Imperial gods. Perhaps the College teachers even outnumbered the traditional Greybeards, and therefore were able to usurp Kyne's importance in High Hrothgar in favor of Kynareth--perhaps not even purposely, but rather as a matter of course.
I personally like this theory because it explains two things at once. That said, it is a huge stretch of the imagination to assume that the Greybeards managed to lure the College teachers to High Hrothgar, persuade them all that they were wrong, and then teach them all to be the Tongues they purported to be already (unless, of course, YR is lying; as an Aldmeri citizen and relative to an uncle who has connections to the Thalmor, his perspective is just as skewed as the PGE's, just in the opposite direction). That said, I'm sure being introduced to a live dragon who is willing to teach them in return for their adherence to peaceful uses of the Voice might have helped persuade them. Then again, the player character Dragonborn is a lot more important than some idiot sods pretending to be great warriors, and they won't let us visit Paarth for ages--somehow I don't think these piddly little false-Tongues got an invitation any more quickly than we did.
Again, it's all speculation, but it would be nice to have an explanation for the Greybeards' attitude toward divinity that actually explains something else about the game world as well.