Balance
There are hundreds (thousands) of Jedi. The Republic is at peace under thier guardianship. There are only two Sith. They have to work in the shadows, behind the scenes. I read the whole balance in the force thing as "be careful what you wish for, you may get it". If Anakin and the Palpatine kill all but two jedi (Obi Wan and Yoda), and takes his place at Palpatine's side as he will, there will be balance. 2 Jedi and 2 Sith. Of course, those 2 sith would now have the might of the empire to wield, but the force users (Jedi and Sith) would be in balance.
Later, Luke fixes the problem and restores imbalance (good over evil) in the force.
I don't remember them saying that the Sith brought imbalance, just that someone would bring balance. They seem to think this would be an improvement over the current situation. If they did say the Sith brought imbalance then that shoots a hole in my theory :)
Also, I don't think Luke (and Leia) are clones. It is unclear when Vader finds out Luke is his son (or if he knew all along). Maybe after the end of Star Wars he did some investigation and found out he grew up with his half brother on Tatooine and put it all together. And cloning wouldn't explain Leia (or would it).
