Thanks, vaiderios! :)
You refer to the order of viewing the movies, but let me ask, have you ever watched them in the order 451236? In that order, for a first time viewer, you can experience just about ALL the surprises. You get the "I am your father" surprise without spoiling the "Henceforth you shall be known as Darth Vader" surprise.
Well, I think that Episode V kind of spoils the "Henceforth" sequence, because it becomes clear that whoever guy whose last name is Skywalker but first name is not Luke is his father. Well, as I said, the Order I first watched them was 145623 and then I was just randomly viewing movies.
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I will most likely keep the TPM beginning idea, it feels like it will work out pretty well.
I also noticed another parallel in TPM/ANH: Qui-Gon and Obi-Wan are those who get Anakin and Luke respectively started on their journeys, and they are meant to be their teachers and masters, yet they die before they can do anything, so Anakin is trained by Obi-Wan and Luke is kinda trained by Yoda. But Luke hears Obi-Wan from time to time, Obi-Wan acts like his Guardian, if you will. Now, what if Qui-Gon acts as Anakin's Guardian? What if Anakin hears from time to time Qui-Gon as Luke hears Obi-Wan?
It's not a problem to add Qui-Gon's (after his death, of course) phrase "May the Force be with you", though it would be more nice to cut out a "The Force will be with you. Always." phrase. I think it would be nice, if done properly.
And I think Liam Neeson filmed enough footage in other movies that would make themselves appropriate so he could talk to Anakin EpII and III. About Episode III, you all know about the voice of Palpatine in the JEdi Council room, when Anakin makes his final decision. At first I wanted to remove this voice, but then I though, what if I were to add Liam Neeson as Qui-Gon? Maybe even make sort of a conversation. But as soon as Anakin becomes Palpatine's apprentice, Qui-Gon doesn't talk with him anymore. Until either Episode V or Episode VI.
Now, there's one instance in Episode V where I can see Qui-Gon's voice fittable, it's after the talk with the Emperor (it's possible to tweatch the scene so there wouldn't be a swipe right after it ends and add a little more time). Maybe as something as simple as "Anakin?" (or without the question mark). It would work really well with Vader learning that his son is alive only at that precise moment. And this could be marked as the moment when Vader begins his journey back to the lightside (just as Anakin's path towards the Dark begins in AotC), when he starts to remember his old self and has gained again something to live for, even if he doesn't fully realize it.
Episode VI has more instances where Qui-Gon's voice could be seen as appropriate, I have to think about it. I do have an idea to add Qui-Gon's phrase from Episode I, which he'll certainly say to Anakin in my edit, which is "Always remember, your focus determines your reality", at the moment when he looks at Luke being tortured by the Emperor. And after this, Anakin understand that "Screw everything, this is my son, I couldn't have saved Padme, but I can at least save him" and goes wild on the Emperor. I think this idea looks good, at least on paper. But, as we all know, not everything looks good on screen as it does on paper.