In terms of using what already exists on film it's more problematic than my idea of having the Neimoidians trying to reclaim a planet they were kicked off from centuries ago by the Naboo.
Cutting the Gungans out of the film leaves a big hole with not much to fill it with either.
We don't see any evidence of cloning in TPM, we don't see much evidence of hardly anyone on Naboo for that matter. You can't just shift material from AOTC in there either because then you make an even bigger hole the next time around.
It is surprising how through a mixture of re-dubbing and editing how less stupid the Gungans become.
Naturally it would be ideal to replace them with something totally different and this is the radical redux thread so I'm all for ideas on how to do that but it might be more practical to make what's already there work better.