Some great ideas fairuz! Definately some thinking outside the box on your part. I like how in the early clip you cut the introduction down to just Obi and Qui-Gon. Also interesting to see the idea of cutting into the cockpit earlier in the ROTS opening. However I'd suggest doing the cut when the camera zooms in close to Kenobi's fighter at 00.40. This would feel more natural and preseve the elegant sweep of the original 'waterfall' opening shot.
I have re-dubbed all the Gungans (With new subs), turned Anakin into a hero, restored deleted scenes, re-arranged the final battle and drastically recut Kenobi's duel with Maul, in my edit(Among other things). So I can testify that they'll also work for you too as you suggest.
In my experience video edits are easy in comparison to audio edits. You can be quite bold with the visuals but if you can't back it up with the audio you've got a problem. I've been in plenty of situations where I wanted to cut something a certain way but couldn't because the audio was unfixable*. So to save yourself time and energy I'd be mixing the audio as you go.
* e.g. Jar-Jar juggling in Watto's shop. You've just faded it down. I gaurantee unless you totally recreate the soundtrack including hiring a Liam Neeson impersonator, you won't be able to sort that like you want to... I tried, oh boy did I try :-)