There were no Matrix sequels... Lies, I tell you!"
Agreed. Matrix should have stood alone. The effects of the sequels are great, but the storyline is nowhere on the same level.
"If he could be turned, he would be a powerful ally."
Why the hell would the Emperor agree to Vader saying, "If I killed you, he would be an acceptable replacement"?
Well, he did say "ally", rather than "apprentice". Even before the Rule of two, it's clear that Vader wants to save Luke because he is his son, which is motivating him to act against the emperor. On top of this, Palps obviously sees Luke as a threat to be eliminated in the first place.
"According to George, the rule of two went into effect after the Sith were wiped out, which menas, the only way Yoda could possibly know about it would be if he, himself, were the Sith Master."
I agree this is a plot hole as well. I think Lucas just threw this in for the audience, and it's gonna be glossed over.