So, just because you don't like the themes or don't interpret certain themes the same way, does not mean those themes do not exist and were not intended by the creators.
The original novel Jaws was a tale of greed. Same with the movie. That was one of the main intended themes. You can choose whether you think they effectively communicated that theme, but you cannot dismiss the author's intention. Though if you clocked the mayor as a villain, I'm pretty sure you got the idea and just don't like that interpretation.
I think it is pretty clear the novel and the film are trying to tell the audience the mayor prioritized economic interests above the safety of actual people. You could even draw environmentalism parallels where corporations will pollute and make people sick despite the harm it causes.
You can't say it doesn't have those themes because the story would play out differently in reality. That's why it's called a story.
Top Gun was a Navy recruitment film. Literally propaganda. The filmmakers got unprecedented access to military assets and in exchange, the US Navy was allowed script approval and even demanded changes. It is estimated the original movie caused a 500% increase in recruitment. It's still a good movie and I loved the new one too. But I think people need to be aware of the military recruitment goals baked into the story.
The Matrix is a little more nuanced. Some of the trans themes that many see as overt in present day were probably only intended on a subconscious level when The Wachowskis were creating the films.
However, coming out as trans is not a thing where you suddenly go, "Oh wait, I'm trans!" Most trans folks have feelings about their gender as children. I think it would be impossible for them to create something that personal to them without the allegory being influenced by their feelings about their gender.
Beyond that, there were definitely very intentional trans aspects to the film. The red pill was based on Premarin which was the estrogen used for HRT during that time period.
Taking the red pill begins your journey to living in a new reality.
Yeah, nothing trans about that.
And the character Switch was intended to be a man in the real world but a woman in The Matrix. They were unable to get corporate approval for a trans character, but I think if you look at the way Switch presented herself in the movie, you can still see the original intention of that character.
You can watch the video above and see what Lilly has to say about it and decide for yourself, but I think there was definitely some strong subconscious intention behind the trans themes in The Matrix.
And I think the pill and Switch show it was definitely on their mind back then.