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I thought of it before. The problem is nes textures have only color indexed (0->3) on actually color. We have to convert it to 4 basic colors for example black, red, green, blue while exporting and reconvert back to indexes while importing. We can see that it's not straight forward process but it's still worth the feature though.

i figured that while the color indexing might be a problem, it'd be less of a hurdle than trying to add stuff like free select/magic wand into the texture editing interface within unity.

Yeah, for big texture editing we should support import/export