The thing that bothers me is where the cuts (referring to Vader's) are placed: right at the point where the final reel starts.
For those of you that haven't seen "Fight Club," those little dots in the corner of the screen are called "cigarette burns." They appear five seconds before the end of a reel and at the very end of the reel and were originally done so projectionists would be able to switch reels at the precise moment necessary in order to keep the film rolling without anyone noticing what was going on. This system (of a manual reel switcher) isn't used a lot anymore, but the cigarette burns have remained as a guide for the person assembling the reels into one huge reel at their respective theaters.
Okay, that aside, the final reel change on Episode III occurs at the precise moment that Obi-Wan slashes through Vader's legs and arm. It's probably the worst placed reel change I have ever seen in my life and I'm looking forward to the DVD just so I can see it without the huge "film jerk" that invariably occurs at every theater I've seen it in. I think that the reel change is leading to a lot of this confusion (e.g. when Obi-Wan takes out the left arm) because not only are you having to pay attention to the action on screen, the reel change runs a kind of subconscious visual interference that makes the action even more difficult to follow.
The cigarette burns also fall into the category of things you notice once and you NEVER stop noticing for the rest of your life. Thanks Chuck! Thanks David! Thanks Brad!