The dialogue that you've patched together works really well!
When I watched your clip, I didn't want the scene to end! I really miss Qui-Gon from the PT and it was cool to have him "back".
The line "You still have much to learn, my apprentice." Doesn't work as well, in my opinion.
I guess having Qui-Gon call Yoda "apprentice" is odd. I guess I can't really say why. I just don't think of Yoda as an apprentice.
Could it be "You still have much to learn, old friend." Or "...master Yoda."?
Yeah, I would take a listen to Batman Begins and see what might work there.
I would encourage you to try and extend the dialogue between the two...it's just so cool!
This idea just came to me:
Qui-gon: "He IS the chosen one."
Yoda(from ATOC): "How can this be?"
I liked SOME of the cutting back and forth between Yoda and the visions, but it was slightly over done.
I'm also not sure about some of the clips:
Clones: Why clones?
Padme: We're gonna see her in a sec.
Luke: Let's not "ruin" the iconic shot from ANH.
"Also, do you guys think I should pull that short clip of the skiff flying away from Mustafar (the unused one). I tried extending it but it got all weird and blurry... I kinda like that shot..."
Yes, I would cut it. But if you feel it should stay, you should at least flip the shot for screen directions sake.

Gotta go!
Again, great stuff! Please continue!
