hairy_hen said:
Simple: don't show it.
More easily done by having Anakin Skywalker not be the main character, and occupy less of the focus. Neither would Obi-wan exclusively be the protagonist, so that the fight which leads to Vader's need for the suit of armour isn't really shown either. This allows Anakin to 'disappear' from the story, say at the end of Episode 2, without being fully explained; and Vader to appear as a menacing and mysterious villain who hunts down and destroys the Jedi in Episode 3.
Well, then, who should the main character/protagonist of the prequel trilogy be, in your ur opinion???
Darth Vader just killed a group of younglings Jedi and Cin Drallig and his 2 padawans, during/Episode 3 revenge of the Sith, and a few other knights/masters if you bring up the EU (the expanded universe, like the novelizations and stuff). He did kill a lot of the Jedi in the jedi temple, they just didn't show a lot if it to the viewer.
A huge flaw/plot hole is this. We never saw anakin skywalker/darth vader actually kill a lot of Jedi in person on the big screen, it was either shown in a hologram, implied with the youngling scene, or mentioned in the Eu expanded universe. No scene where he actually takes out his lightsaber and goes after them.
Order 66 was so wasted in the star wars prequels trilogy because, for Christ's sakes, the movie was 2 hours hrs long or so, you can't add a few minutes of darth vader killing some jedi???
Besides, "at last the jedi are no more". Wait, that contradicts the EU the expanded universe, because there were surviving jedi hiding on/in that mining planet Kessel and the wookie chewbacca planet called Kashyyk......