I'm pretty sure in the 'Sith' commentary Lucas states that it is the Death Star from 'Star Wars.' At least I am positive that he doesn't say that it is a prototype.
Maybe it didn't take 20 years to roll out. It could have been completed and then tested or put into hiding for a long time. They probably don't take too long to build because in 'Jedi' the opening crawl states that the Emperor had secretly begun construction of a new Death Star after the Rebels destroyed the first one. Death Star II was almost completed by the time of the Battle of Endor.
If anything, the Prequels proved that Palpatine was all about the cloak & dagger - he tends to bide his time until he is ready to strike, which is why I favour my theory that it was completed and then sent into hiding. They obviously saw the Rebellion as a threat so it would make sense to keep it out of public knowledge for a while.
Then, when the Emperor is ready to tighten his grip on the galaxy, he unveils the Death Star and instills fear, which, is the ultimate weapon of control.