So I have this greninja with a bad nature that I want to change. But it's the one I use in ORAS battles. Also its pp is nearly maxed. Is it worth changing its nature?
No. It's not worth changing after all of your hard work. Stick with it through good and bad plus its got better pp.
It depends on the nature, since some natures could be not the best but still workable with, and the kind of greninja you want.
Max PP isnt a big deal. If you dont have 5-6IVs or a good nature, I suggest breeding a new one. IVs and Nature can have a big impact on your greninja and you'd want them to fit the team and set you are using.