Alright in the Prequels, the Jedi Order gets wiped out pretty quickly. The whole Order 66 was interesting (for me anyway since it was based on the real life Executive Order 9066 that brought the Japanese Internment). However, I felt it was just too quick and sudden. It didn't make sense to me since the Prequels didn't explain why the people were just okay with the Jedi Order's sudden demise. It didn't help when I notice some particular bits from the EU novels that touched on the subject.

Here's a small excerpt from The Last Command of the Thrawn trilogy:

C'baoth snorted. "The Jedi Master Joruus C'baoth does not serve lesser peoples, Jedi Skywalker."

"Why not? All the great Jedi Masters of the Old Republic did."

"And that was their failing," C'baoth said, jabbing a finger at Luke. "That was why the lesser peoples rose up and killed them."

Here's another from the Darth Plagueis novel:

Sidious took a moment. “We will have to exploit their vanity and blind obedience to the Republic,” he said with greater confidence, and as if the truth of it should be obvious. “They must be made to appear the enemies of peace and justice rather than the guardians.”

The prequels do not do these two excerpts justice. The demise of the Jedi Order could have been handled a lot better than what we saw. How to go about it, that's the main question as there are many ways.

You could:

a) Let it be like the Templar's fate where the Jedi are false accused and hunted down for a crime (possibly treason).

b) Show the people slowly staring to hate the Jedi until they turn on the Order.

c) Have the Jedi Order rebel against the Republic/Empire (depending on which version you use) and the Jedi are wiped out.

However, those are just my ideas. What would your ideas be? Please let me know. Thanks.