It's not just the Emperor and Vader they have to be stronger than to win. It's the entire republic army, which as you see with Order 66, can take out a hell of a lot of Jedi. They split up and went for Vader and Palpatine because they still had the element of surprise. They didn't kill either, and there was not yet a rebellion to back them up if they tried again.
This is more speculation/opinion on my part, but there's also a parallel in their hiding. The Sith (Bane through Sidious) had an entire galactic regime (the Republic) opposed to them, so they hid, in small numbers, biding their time and waiting for the right moment to strike. To beat the Emperor and his forces, the Jedi do the same, though much quicker.
