I'm agreeing with lantz, Black. Your post is definitely... interesting. I read it with Vince Offer's voice in my head.
I don't really see the point in asking anyone's canon, because it seems to be to be the same question as "what's your favorite route?" which seems to be the same question as "what's your favorite pairing?" Well, I'll answer anyway.
For KnK, like mentioned above, there are no "routes" to speak of, and there is only that story, which actually may possibly be my favorite Nasu work overall (certainly parts of Tsukihime and F/SN beat it, but not the whole of either game).
My canon routes, strangely, don't really line up with my favorite routes in the game. I actually sort of pick the Fate route and Arc's True End, despite my favorite F/SN route being UBW (I actually really do like Arc's route in Tsukihime, because the romance in that one seemed genuine to me, and not just like "oh, we need to have sex or you're going to die").
My reasoning is thus: Due to the nature of a Kinoko Nasu multi-route VN, there will always be one route that establishes the setting and introduces the major characters and themes. Then you have the middle routes that start to complicate the characterization of the characters and revealing backstory on others while still keeping more or less the same theme. Then you have the final route(s), which totally upsets everything that was established before, takes the remaining minor characters or introduces brand-spanking new ones, and uses them to twist the original thematic tone of the game towards something much darker and more depressing, upsetting the uplifting conclusions drawn in the previous two-thirds.
Then, Nasu will give that final route the happiest ending of them all. Because fuck consistency.
So, I can't take the final routes as canon, because they cannot stand alone at all. They require a read-through, and not just in summary, of the first and middle routes. Ditto for the middle routes; they stand up a little better than the end, but still benefit from the first route establishing the universe.
That's more or less why I think the first route of any given game is canonical.