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So one thing. The whole Golems vs the Spirits thing lends itself to a very cut and dry nature good, machines bad motif. Which isn't exactly a bad thing but I think it would be better if we could avoid it.
There's a real opportunity in Industrial City in particular. A large, urban environment full of industry that is perfectly peaceful. There can even be lines referring to how they (as good guys) are responsible about how they go about things, which only makes the bad guys seem more like dicks.
Stuff like sending extra metal to the scrapyard to be recycled/eaten. What industrial waste they do create they make sure to keep contained in the sewers, which poison pokemon have adopted as their home.
And even if it is a bit slumish or littered in parts there could at least be people saying they are working at making it better
