The Natives planned to bring world peace by turning all of the humans into Natives, wouldn't that just make it so all of the wars were being fought between Natives rather than humans?
Maybe changing humans to natives works the same as the copying Worm do. When a Worm copies a human, the Worm still has a singleminded insectlike way of thinking (With the exception of those higher up worms, who sometimes seem more intelligent than your average human, but they can be compared to the queens of an insect-colony). So when a human changes in a native, so does its way of thinking. The victim will think Negishi/Mishima(whoever was in charge wasnt clear) is his 'queen' so will obey him every command. That way they will stop all wars, because everyone would be part of the same 'hive'. The Natives that get humanlike traits(like tadokoro) will be easily eliminated in the new Native world order.
Maybe. Negishi's reasoning was that the conflict was born from the racial divide between humans and Natives, so he tries to remove the source of the trouble by eliminating the racial divide altogether. It's not the most brilliantly developed plan, but that's a hastily tacked-on Big Bad for you.
There's villainous subtext there that probably wasn't being said outright. The head Native(s) probably had a way of trying to bring all other Natives under their control. There would be world peace because the entire population of Natives would be enslaved to a single ruling body. Basically it's genocide and fascism rolled into one convenient package.
So... where the heck did the hopper zecters come from?
How the heck was Kabuto able to defeat Cassis Worm Dimidius? I mean yeah, he hit it with a hyper rider cyclone, but that worm's clock up could practically freeze time, even for Hyper Kabuto! Why would it ever let itself get hit by an attack like that? Also, just before defeating Dimidius, Kabuto mentioned that he had "figured out [Cassis's] trick". What was he supposed to have figured out that allowed him to counter a time-stopping ability with essentially no effort?