Stuff in episode III that needs to be reconciled in the EU
here's what we've been told so far-
The Republic is some 25,000 years old.
The Sith were wiped out at the 7th battle of Ruusan a thousand years before episode I. Darth Bane survived and started the rule of two, and the sith were hidden until the revelation of Darth Maul.
Now, contradictions-
Yoda knows the rule of two and mentions Darth Bane by name. The Jedi also apparently own several of his holicrons.
Palpatine mentions that the Republic has stood for a thousand years.
The Sith had tyranical control over the republic before this time.
and finally, Yoda seems far too confident when doing battle with the sith, he knows their tactics, their fighting styles, and even how to absorb and reflect force lightning.
Now, my consolation of these contradictions-
10 years after the battle of Ruusan, Darth Bane and Darth Zannah had managed to infiltrate the inner circle of the supreme chancellor. They then began to control the chancellor through the force, managing to raise a secret army of some kind, possibly an order of minor sith knights (not technically violating the rule of two sithlords, similar to the plan that sidious detailed to dooku). They then assassinated the chancellor and the senate. usurping power on coruscant and expelling the jedi (since they didn't have the numbers to wipe them out). After a decade of oppression on coruscant, a rebellion of other planets joined by the jedi liberated coruscant and reestablished the republic, killing bane in the process. over the next two hundred years, the sith were hunted to extinction by the Jedi with Yoda killing the last of the knights and what was assumed to be the last sithlord.
But how did the sith survive? either this sith feined death or broke the rule of two. or perhaps he switch places with a minor sith knight. Then the sith stayed in the shadows, having stolen much knowledge from the jedi temple during their rule. they knew about the prophecy of the chosen one and plotted on how to take over the galaxy, exterminate the jedi, and either convert or remove the chosen one...
so that's my theory.