That's an interesting idea about the Neimoidians being worshipped as gods...has a Stargate feel to it. It could work by using subtitles for Neimoidians and Gungans, but it would be tricky. How can that be developed and tied into the reason they're invading?
Alternate history time.
A longer time ago in a galaxy far far away....
The planet Naboo was home to the Gungans, a relatively primitive race.
The Neimoidian Federation was at war with humans who were expanding into their sphere of influence.
The Neimodians colonised the planet as a staging post during their war, the Gungans saw their advanced technology and believed them to be gods.
Eventually the humans drove the Neimodians off the planet and claiming it for themselves.
The Naboo and the Neimoidians later became members of the Republic but the defeat entered into the history books of the Neimodians and the resentment remained (it became a cultural yearning to reclaim the world even thousands of years later, there are plenty of real world examples).
The Gungans developed their own advanced culture along side but seperate from the Naboo, partially enhanced by studying technology left behind by their Gods.
Initially they resented the Naboo for driving their Gods away but thousands of years later the reasons for their resentment had largely been forgotten and developed more of a cultural flavour.
The Gungan religion remained but when the Neimodians returned the Gungans were too sophisticated a race to see them as their Gods of old.
Palpatine played on these ancient feuds to spark one side of his phony war.
If Nute Gunray could reclaim Naboo legally he would return home a strong leader who has returned a long lost province.
The Republic would be thrown into chaos because one member race has attacked another and the Senate has done very little to nothing to stop it.
The Trade Federation could even use the Gungans to legitimise their invasion, claiming falsely that they are a force of liberation returning the planet to it's indigenous people (which would give Jar-Jar more of a reason to be in the story).