I had several relatives who had not seen 1 and 2, but loved 3. They went back and watched 1 and 2 afterwards and got all confused by all the unresolved plotlines they caused. I found it funny that they all think 3 works better if you've never seen 1 and 2.
Agreed. And its not just plot points; take the Anakin/Padme relationship, for example. Their scenes together are quite good in 3, but audiences moan and groan regardless due to the evoking of memories from 2. If you just see their marraige and interaction from 3, you can imagine the rest, but it's ruined by their botched "romance" in 2.
And, Hardcore Legend, the concept of your scene alteration is good, but it makes no sense story wise. This Vader character comes out of nowhere, asks about Obi-Wan, and Palpatine tells him he killed him? There are a variety of ways to do something along the lines of what you're talking about to improve the scene, however, depening on how you want to approach the Anakin/Vader thing. Asking about Obi-Wan is good, as it makes sense for Anakin to do so considering not too long ago he was the one who mutilated his body. If it could somehow be established they think he's dead/in hiding that would answer a plot hole or two. Then he could ask about Padme, and the scene could continue as nomal, with whatever changes are necessary to make the last shot more respectable. My suggestion would be slowing down the footage so that Vader is not swaying back and forth and combining the "NO" with a couple of other Vader grimaces from the OT, making for a tremendous, unintelligible noise.
For example:
P: Lord Vader? Can you hear me?
V: Yes, my master. Where is Obi-Wan?
P: Hiding. It is of no concern. Soon the Jedi will be wiped out, and we shall have have revenge. (Pieced together from various Palpatine dialogue)
V: And...Padme? Is she safe? (scene continues as normal...)