"Always two there are." - The concept of only two Sith at a time
This is just baffling. I mean the Master always has to be on the lookout because his apprentice will try to overthrow him some day, right? That's a great way for an opposing faction to cooperate. And this extinct-for-1000-years stuff is too far fetched. Imagine generations of two Sith Lords debating in hiding about when is the right time to reveal themselves.
"Hey Darth Random, how long do we have to wait to reveal ourselves? I made this awesome lightsaber and i wanna kill some jedi!"
"Patience my young apprentice. We, the Sith, disappeared 500 years ago. Let's wait another 500 years to trick the Jedi into thinking we won't show up any more."
"Waiting sucks."
Make it a hundred years and it feels more comprehensible about a bunch of evil guys slowly infiltrating the Republic.