I have an idea to use Nute Gunray who wants to assassinate Padme by recruiting a bounty hunter, the beginning of the film will start as AOTC, at some point in act 2 when Padme and Anakin leave Naboo to go to Tatooine I plan to insert the invasion of Naboo by the separatist alliance there.
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I am currently working on a similar fan edit.
And I believe that a good way to connect the two movies would be a plot by the Trade Federation that intends the attack on Palme to fail, to force her to go to Naboo into hiding, so the Trade Federation can take her hostage.