Spoilers all around.

I agree with you on point 1, although I think she hinted that the choice in question was her decision to point Neo at the Merovingian. So he probably had her eliminated. Nevertheless, I'd like her to at least explain how she came to find another shell and didn't get deleted all to heck.

Point 2 - the Architect never suggested that Zion is another part of the Matrix. Rather, he said that Zion was used as a part of his equation to ensure the long-term stability of the Matrix. I watched Reloaded carefully a couple of days ago, just to make sure I get everything the Architect said before I see Revolutions.

As for point 3, I actually thought that the deeper delve into the characters at Zion was a very good idea, given the ending. If we have Neo sacrifice himself for Zion, it's important to get the concept that there are real people out there, that really needed the sacrifice of our favorite character. Now we can think "He sacrificed himself for Link and Zee", rather than just for the general concept of freedom.

Point four: the ghosts? You mean the twins? They weren't ghosts, and they never died. They were just nice programs who had the ability to transmute into a non-corporeal manifestation when they wanted. They never actually died in Reloaded. You can see them fly out of the wrecked car.

5. I think they are holding out for another sequel - the studios would probably not give such a golden egg up without a fight. So they put in some leads for a sequel.

6. I never thought about King Arthur. That's interesting. So Smith is basically Mordred.