One thing has bugged me, in terms of fitting in the established EU with TPM and AOTC: the Jedi Order doesn't follow the same set of rules as the Knights prior to 1999 (both before the Clone Wars and after Endor).
For starters, the old-school Jedi had no problem with marriage. They also frequently trained multiple apprentices (the word "Padawan" never pops up), most of whom were selected as teens or adults. And every last thing they did (missions, choosing apprentices, etc) didn't have to go before the Council.
I think I have it figured out. (And, like my lightsaber color explanation, I'll believe it until Lucas himself tells me otherwise. )
Obi-Wan in ANH calls the peacekeepers of over a thousand generations "the Jedi Knights," not "the Jedi Order."
There are also only 20 Jedi to leave the Order. Any one installment of "Tales of the Jedi" features about that number of fallen Jedi alone. (And I don't recall seeing Exar Kun or Ulic Qel-Droma among the busts in the library.)
So there is no reason why the Order isn't a much more recent development than the Knights themselves.
As recently as 1000 years prior to TPM, the Knights seemed to be a somewhat disorganized group. Did the Order and its doctrines come into being to prevent Jedi from falling to the Dark Side and starting another Sith War?
I think the beaurocratic mess we see in TPM and AOTC (and, presumably, ROTS) came into being within Yoda's lifetime, or only slightly before. And it involves too much red tape for the Jedi to even see they're in tremendous danger from the re-emergent Sith.