One could conceivably split the whole thing into two. Perhaps the initial "war" occurring during the first film that's a relatively short and localized conflict involving a smaller force, which is defeated by the film's end. While most of the Republic (including the Senate) write it off as a relatively minor incident, Yoda and Obi-Wan sense that its not the end.
Then in the next film, the second war starts with a much bigger army leading to a far more drawn out and destructive conflict with the battles in the first movie placed in the context of being just a test of the Republic's strength.
I also have to second Mrebo's thoughts on the Sith. I think it makes for a more intriguing and thrilling story if the Jedi aren't really aware of the sheer scope of what they're up against until its far too late. It creates a tragic but understandable picture of the Order not having dealt with any real dark side users for such a long period that the Emperor's emergence as an evil wielder of the Force caught them completely by surprise. (Perhaps doubly so if the Jedi think Palpatine's little more than a crowd pleasing populist who not too different from previous bureaucratic Presidents in the Senate).
And maybe this is stretching things too far, but it may explain things about Anakin too. Perhaps he didn't really get enough teaching about the dangers of the dark side, simply because it had been so long since the Jedi had seen anyone turn and/or encounter those who could potentially seduce students to turn from the light side.
If there aren't any Sith running around, it would also serve to strengthen the relationship between Palpatine and Anakin if the former wasn't looking for a replacement apprentice, but actually saw something in Skywalker that made him realize the value in having a second in command who could wield the force, period. No rule of two, no Sith tradition; just a cunning dictator who realized the perfect weapon to destroy any Jedi opposition.
Now the scenario from ROTS is much more convincing: a young, conflicted Jedi with the force flowing through him, lacking the true knowledge of the dangers of the dark side, being shown powers and possibilities he never before imagined by someone who's given no indication of hostile intent. Seems like an ideal situation for seduction to me.