I've always felt that there is more of a surprise in store for the audience in the OT having seen PT Yoda. At first you're in shock that he has gone nuts. Then you're surprised that he hasn't actually.

A lot more than most people here, I find that I'm happy seeing anything done to ANY of the films to make them work as a 6-part series. The truth is that the PT sets things up on a very huge stage, and the OT really presents a much smaller, focused world. Yoda as a "distant, unseen" mentor is hard to buy for three full movies (and an absence in the fourth) when space travel seems so easy and to take almost no time at all. Sure for a couple movies, you can do that, but then you expect to see some sort of interaction with this far off character.

Perhaps Yoda could be in his home on Dagobah during the events of The Phantom Menace, shown only through a hologram, up until perhaps the ending of the film. The Sith returning would flush him out of solitude, at which point he would return to the Temple for the rest of the PT, until he is defeated in Ep. 3 and returns home, now exiled.

It might be cool to see Yoda in his hut, with a hologram of Anakin as a boy, giving his "Fear leads to anger, anger leads to hate, hate leads to suffering" lecture. You could switch back and forth between the council room and Yoda's hut throughout the scene. Yoda scenes would be much easier to film as well, I would think. You could show the back and forth for nearly every sequence he is a part of.

He then is shown leaving Dagobah on a ship right around the time that Obi/Qui-Gon head back to Naboo. That way he has arrived in time to be at the funeral, and to tell Obi-Wan "Your apprentice, Skywalker will be..."

an added sequence somewhere in there could have a Samuel J lookalike (or some random Jedi) asking: Master Yoda, if this is true, what must we do?

"If return, the Sith have, my time to return, it is as well." It could be built up to a huge moment, with some sort of triumphant return music.

Just a small thought ;)