Remember folks, the "Rule of 2" didn't exist until Episode I was written. Who is to say it's still in effect now 24 years after the Jedi were destroyed and the Sith have taken power to "rule the galaxy"? There's no need for the rule anymore. When Palpatine is saying he would be a great asset he's not implying he's going to replace Vader or himself... he's saying there will be three! If you want to get even more nerdy, in the Expanded Universe both Palpatine and Vader had dark side apprentices during the OT era. This "well you have to constantly be trying to kill your master to advance in rank" thing is pure BS.
The original intention of the scene has always been that the Emperor is scared of Luke's increasing power, he wants Luke dead. Vader knows very well he has a son and wants that son for himself. So he persuades the Emperor to let him turn him to the dark side, to keep Luke alive. Vader's secret plan to use Luke might be a ruse, or it might be Vader's own ambition. Let's for once see the Emperor not totally in control, manipulating everything with plans within plans within plans (like in the Prequel trilogy). ESB is not the Emperor's movie, it's Vader's. Let him have his moment and be in control, even while this shadowy boss is now being mentioned.
Yes, by ROTJ, Palpatine wants Vader turned and the relationship is starting to get ambigious, but not because Palpatine wanted Vader dead all along. He doesn't possibly suspect anything until "I wonder if your feelings on this matter are clear." I frankly think the idea that these men have been working together for 24 years with loaded guns pressed to each other's heads the whole time is just stupid. Why can't bad guys be loyal and then later events start to shift those loyalties? I don't think it's a problem to have the Emperor one step behind Vader until the very very end. He's not infallible.
Palpatine trying to replace Vader later on in ROTJ is just a spur of the moment thing. Vader has been beaten and he's so enthralled with Luke's demonstration of power, that he just wants him to take the next step (killing a downed foe in a fit of rage, and obeying the Emperor's command would push him over the edge and into the Emperor's control as a dark side minion). It's not because "its the Sith way to try to destroy ourselves constantly." So people take it too far. There's no real need for a contradiction. Just say the rule of 2 served its purpose and now it's over with. Remember, even in the Episode I novelization where all this new backstory is created for the Sith, the original Sith had thousands of members, and that was when they were fighting the Jedi (there's no Jedi to oppose them now, and no infighting). It's just that good force talent is hard to find these days...
As for Palpatine's "180 degree turn" in this thought... in the 1980 performance it is much more believable because when he says "yes... yes" it sounds like he's really thinking about it and liking the idea more and more. In the 2004 edition the way he says it is just like he's like "okay, whatever..." almost like Vader has hyponotized him for a second there or something. Not much that can be done with his voice though I don't think.
The "interrupting clip" while a neat idea, I think again just diminishes the scene. The lines were so good to begin with, to have any of this sort of thing is just off. The Emperor's character has already been established. The only time he ever interrupts somebody is in Episode II where he finishes Padme's line for her. Clever, but I think it just further tarnishes the scene to try to do more with it than is already there. The only thing that really "needs" to be changed is to make the hologram actually look like the Emperor we all know and love (ROTJ) and sound like the actor who portrays him. Adywan was on the right track with his teaser. He just needs to do the side view and the rest of the (1980) lines. If he says "Luke" it's already better than the previous attempts at doing this scene with the original lines in Ian's voice.
My 2 cents.