I think Yoda should be in the prequels Suppose you're watching the saga in PT-OT order. You'd find it weird if when you're by the fifth episode this green old jedi master from the republic era shows up. It'd be like "hey, i've seen the republic era, and he wasn't there!". Tough I must say, my idea of what Yoda would do in the PT is quite far from what he actually does.
In that way, several things in the prequels should be adjusted to OT; think how unreknown the Skywalker surname is within the Rebellion, in spite of the famous-glorious (?) Commander Anakin is supposed to be in the PT... Though it'd somehow make richer the plot of ESB if Luke was asked several times if he was the son of the historic Anakin, it'd make us wonder who the f*%ck Anakin was, til... and then... off topic (?)