I have been talking briefly about this idea in the prequel ideas thread, but I think associating the separatist with slavers could really benefit the story, making the whole conflict feel a lot more personal to Anakin.
So what if the gungan are the reason the federation chose Naboo? This could be explained with them wanting slaves that can operate under water or something.
It would both connect Anakin’s story to the overarching story of TPM and add a lot of emotion to the battle between the gungan and the federation army to a point that it would almost exactly parallel the battle in Spartacus, which it optically already does.