because as was discussed, i think most of our ideal prequel stories would not contain the planet naboo so it becomes a non issue.
buddy-x-wing, i have not seen the clone war cartoons either so this is entirely possible that he achieved the rank of general during this time period. and i guess he did/would have served bail organa under the light that he served the true republic as did the rest of the jedi and some of the senate members who would later have become leaders of the rebellion.
Rebel11_38, as far as the rise of the empire, this is the part of the prequel story that i really like...basically palpatine just slowly gains control over the senate. causes a fake war, where he is pulling the strings on both sides, so when you think about it no matter what side wins Palpatine is in control. also, based on the comment in episode IV about disbanding the senate and the last of the old republic is gone, the idea of the Republic 'winning' against the seperatists really being Palpatine's growth in power over the senate and the republic army. hopefully that makes sense...im kinda tired so it may not be totally clear.
I think part of the problem with a discussion such as this, is that it is very hard to remove ideas that have been introduced by the current prequals from our current thoughts and perceptions. had we done this back in 1998 or earlier the whole of the creative influence would be from us and not influenced by Lucas' stories.
-Darth Simon