I just thought I would makes a reply with some of the things I have been thinking for a while now.
The Clone Wars - most people seem to like the idea of this being the second clone war (because then it shows there is more than one) but I think it should be the 4th or 5th clone war. The reason is that we have had 2 world wars in our recent history, so I think mirroring those but in the context of a galaxy would actually make them seem smaller and less of a big deal for that galaxy. Also if I remember correctly someone made the point that the greater the technology the shorter the war (generally speaking). This could explain why there have been a number of shorter wars, rather than just two very long ones. And finally, by increasing the number of wars I think it allows us to suggest they are becoming a real problem, because although the republic always seem to win the wars, they are not going away. But, I would just like to point out I have no problem with the specifics people have been writing about the war, just think we should increase the number.
The Vader Secrecy - It islooking like try as we might, this is gonna be the make or break point. We have to know (or think) that Anakin has been killed by a 'Darth Vader' but obviously we can't show it because of the small details about it not being your run of the mill death. We then have to have Obi Wan find out the truth, and evenually fight Vader himself, defeat him, and leave Vader with a heavy breathing mask.
To me, the most convincing way that has been suggested so far is to have Obi Wan train Anakin, then to have him train someone else. Anakin slowly and secretly begins to turn to the dark side because he thinks it is necessary to 'interfer' more than the jedi allow. Whereas, the other apprentice seems to take a more obvious slide down to the dark side. Then there would come a point where Anakin and this apprentice fight, they would both fall somewhere. Then by the time Obi Wan gets there all we see is one person putting on a helmet (which we recognise as Vader) but we don't know which apprentice it is. Obi Wan would ask about his apprentice and Vader would reply that 'he is no more'. This way we maintain the secret (to some degree), Obi Wan learns the truth, they fight, etc.
The only real problems I see with this is that if after all this Obi Wan goes to NotPadme and tells his lie, then this could make it seem like Obi Wan doesn't actually know the truth himself. And if Obi Wan has had two apprentices, and both have turned evil, then surely he must have been out of his mind to even think of training Luke himself.
Oh and whilst I am here I might as well make another plug for NotPadme (who I have been naming Lehra) to have jedi training. Using the outline I just mentioned, I would have the Obi Wan vs Vader fight at the end of episode II. Then episode III can be about how Obi Wan, Lehra and maybe a few others would try to stop the other jedi who have left the path. Basically, episode III would show Obi Wan trying to single handedly stop the collapse of the republic and the rise of Palpatine, but obviously it is too much for him. When he thinks he is fighting the leader of the fallen jedi he defeats him only to sense that he was wrong. He rushes off but it too late to stop Vader (who we all assumed to be dead) from killing Lehra. In this fight Lehra would be well out of her depth but she would be incredibly angry with Vader (we would think it is because he killed Anakin, but after the reveal in episode V we can go back and think, actually it is because she realised who he really was). And when Obi Wan arrives Vader would be within sight but unreachable (this way Obi Wan realises he is still alive but they don't fight), and Obi Wan would be more upset about Lehra. She could die in his arms saying something about Vader and Luke, thus forcing Obi Wan to realise he has to stop fighting and run off and protect Luke. Also after Obi Wan witnesses what Vader is capable of, he would have no doubt there is no good left in him, and therefore, when Luke manages to save him it is an even bigger surprises.