What if Geonosis had a Vortex Generator that allowed it to travel throughout space?
I didn't want to shoot down your idea/s brash or ben - it just came out of nowhere, without more context it was a very strange thing (like some others saw it too), BUT:
in light of the more complex synopsis changing "Episode 2" and getting closer to "Hidden Fortress", it's a really cool device ;-)
ever thought, that the "machine" could be some sort of "gravity well" ?
it could explain, why there was "no" planet or whatsoever and it (with some science theory) could explain, how the "planet/oid" can travel from place to place (=> wormhole) - showing up out of "nowhere"!
I think it is important, that in the end this "technology" is destroid, because we don't see or hear about in the OT (maybe in the future if someone is willing to change the new Trilogy)
maybe it could be ancient tech from the Sith / Madalorians - I also thought, that the whole cloning thing could be a paralell to our modern world A-bombs or ABC-weapons ... that it was banned, but the means of an uncontrollable foe / conflict drove the Republic to desperate measures ...
As for Anakin VS Vader: I only found 2 possible (logical) ways to fix that bug ...
A) insert pupil "Vader", name him or not, just show he is around, he is like Anakin is now, not a friend of Obi-Wan, always "testing" him (and maybe "Ani" too) - let there be a duel between "Ani" and Vader, never show who really won, maybe let Obi-Wan know?
B) we have a very twisted soul in Anakin Skywalker, he is/was a good man (and no more boy or kid stuff!) - he is friend to OB1 and they share their part of the Clone Wars(!) - helping Bail Organa and other senators / systems ...
And here is where it gets messy: "Ani" changes through the war/s, he is getting depressed, feeling/seeing (in visions/dreams) a dark shadow looming over him - he belives it to be "death" or some sinister premonition, he doesn't quite understand - so he consults Yoda(?) - here it is like with Luke, that the future isn't static and always moving "bla bla" -.-
But it is even darker: "Ani" has some sort of "shell-shock", otherwise to OB1 he never could shake off the terrors from the battles/fights, they creep into him and there is a part, that likes it ...
hereon you could do anything, just DON'T show HOW "Ani" is turning INTO Vader, make "Vader" the shadow he should be in the PTs ;-)
the bonus? - let Palpatine be a "misguided" senator - and "Sidious" the dark shadow that sucks out life of the Republic ...