Until Diamond and Pearl made everything kind of stupid the games were very much about environmentalism and had a lot of hints about animal liberation, too (somewhat ironically -- I try to keep in mind it is still a video game, after all). The arcs of Mewtwo, Rocket, and Cinnabar are genuinely compelling existential narratives that are only ever hinted at and briefly expanded in the first movie. You do not see stuff like this at all with this franchise, anymore.
For Ruby and Sapphire specifically, this is one of my absolute favorite videos analyzing the historical context around the games' development and what they try to say with their themes. 100% worth a watch if you enjoy the old Pokemon games like me.