My little theory on why His Dark Majesty did not clone Lord Vader, was due to the fact that His Lordship had greater potential than The Emperor. He even said so Himself, in a "conversation" with Master Yoda.
According to Sith "doctrine", there can only be two Sith Lords. One master and one apprentice.
A saying taken from another "nerdy" fictional universe, says that Evil will always turn on itself .This is also true in the SW universe, and "history" shows us that this happened during what was called the New Sith Wars. Hungry for power, the turned on each other, all but destroying their order. And in generations to come, almost every Sith master, met his doom at the hands of their apprentice. The Emperor knew that this would probably happen to him aswell if he allowed his apperentice to become more powerful than himself.
You can read more about the Sith on:
http://en.wikipedia.org/wiki/Sith.