I was going to say exactly this.
A big reason is that WALL-E's main plot is that of a simple love story where the underdog trash-bot has to woo the sophisticated lady droid. It's told without big dialogue. It's physical and works like a silent movie. It's Chaplinesque.
Yet, WALL-E isn't actually as unique if we travel outside of the full-length Pixar films. Pixar's short films are, by and large, like silent movies. They have little to no dialogue and a basic, simple plot.
Now, where WALL-E really shines is its artful, masterly combination of a second plot about the deterioration and potential reclamation of Earth and, as an extended metaphor, humanity itself.
What sends WALL-E into "favourite" status for me is that it manages to weave its "simple" story of love with a complex story of restoration and resurrection.
Combine that with a great aesthetic and a powerful, wonderful message about care for one's self, one's environment, and one's fellow humans (or robots...) and it's a movie that is relevant, uplifting, never preachy, and yet, satirically sharp and cutting in its message delivery.
It's a wonderful film.
Although...the Incredibles is my second favourite Pixar...
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