If you think of the three movies as just one story, dependent of the original trilogy's storyline you are going to have the same problems as George Lucas did.

He first thought what main plot points the trilogy had to have. Characters meet, Introduce the bad guys, Anakin and Padme fall in love, explain the clone wars, Anakin turns to the dark side, Jedi die, Empire is born and the babies are born.

So basiacly he spreaded those plot points through three movies and tried to give it some background storyline... you know:

Trade Routes, Separatists (wich were never explained and never made too much sense), One man controling both sides of a war and The Prophecy.

There was never a good unique storyline on the precuels, and the only good moments of the movies where when they showed the things we already knew.

So if instead of thinking how you can make a whole story out of the three movies (making them dependent of each other), i suggest you do them one by one. Ok, its not bad to think whats going to happen on 2 and 3, but dont try to do a Lord of the Rings trilogy, as just one long movie.

If you make them as independent adventure movies, the REALLY important elements will come along naturaly with it. (Sense of adventure, Good vs evil, Friendship between the characters, pacing...)