I just thought of something about Darth Sidious that's got my mind cranking in overdrive. How do we know that everything going on in TPM is his doing? Ki-Adi Mundi mentions that the Sith have been extinct (and therefore presumably in hiding) for a millenium. Could it possibly be the culmination of a thousand years of Sith manipulation?
In EU, Darth Bane was smart enough to come up with the "only two" thingy. I didn't read Jedi vs Sith (it looked kinda disappointing), but I think he manipulated both the Jedi and Sith armies to wipe out the majority of both. I doubt he'd take on an apprentice who wasn't capable of the same cunning, nor would any subsequent Sith Lords.
If Ki-Adi's number is correct and not an estimation, Yoda's not quite old enough to remember Sith being out in the open. However, he does know that "Always two there are." Was Bane the last Sith that the Jedi knew of? Was someone working with the Sith Lords was interrogated by the Jedi or perhaps word got out through another source?
It just seems odd that the Sith, such a ruthless and power-hungry bunch of folks, would just sit tight and do absolutely nothing for a thousand years. If this is the case, it may explain Maul's impatience a bit better: "At last we will reveal ourselves to the Jedi. At last we will have revenge."