Jumping in late into this thread, but I like the idea of Naboo discovering a new energy source, and the Trade Federation invading in order to take over the lucrative resource, finance the Separatist movement.

The new energy source can be located in the completely out of place generator core that the Duel of the Fates occurs in. This area could be some sort of mining facility for the new fuel source. It's more modern than the rest of Naboo because it is a recent construction compared to everything else on the planet which displays the rich history of a traditional society.

For a real ambitious faneditor perhaps some backgrounds from the droid factory can be added into the generator core scene to make it look more like a place where precious ore is collected. I don't know how feasible that is.

This idea would give a more palatable explanation why the Trade Federation singled out Naboo. Thoughts?