Instead of saving time...
Maybe the crawl in Ep I could state that the seperatist leader, the mysterious Dukoo, is creating clones and that the Feds are playing a double game, threatening to join the seperatists with their droid army if the senate doesn't let them have their way on Naboo.
Maybe alien dialgue could be added in Ep I and Ep II senate to reinforce (silhouette dialogue of Jedi too?) Maybe cut the part of the clones in ST armor on Kamino. Make it seem like the clones are for the seperatists. At the last moment, in the arena, we learn they are for the Republic.