Well, I thought of it as a science fiction film in the way that Star Wars is generally considered a sci fi film. It's much more a throwback swashbuckler, but since it takes place in an off-Earth world of another galaxy, it's "automatically" sci fi, too.
As is Wall-E. Sure, it's of other genres more primarily. But I didn't feel the human story was tacked on. It was the McGuffin and was no more tacked on nor less explored in depth than any classic McGuffin.
It was given more weight than a good many McGuffin, so it veered very nicely into sci fi territory. McGuffin plot was sci fi, and the main characters were all robots. Hmm, yes, love story or not ... this was a science fiction film.
And perhaps I'm giving it too much free parking because it was animated, but I think Alex is also overanalyzing its improbabilities.
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* Just because a movie doesn't show something does not mean it doesn't exist. If the Axiom was shown traveling faster than light to return to Earth, but the probe ship was not ... that doesn't necessarily mean the probe ship travelled at sub-light speeds. In fact, since that's clearly an impossible journey, the fact that they didn't speficially show the light speed portion of that journey means nothing (to me, at least).
* Yes, chemical propulsion was a stupid way to have a giant ship arrive and depart from earth. But it looks so cool. I suppose that's why the Enterprise had shuttle craft and transporters ... but by the time of Voyager, they made sure to land the entire freaking spaceship on some planets because it was irresistibly awesome not to.
We don't know squat about the details of Eve's anti-gravity. Perhaps it only works on small objects, and would be inefficiant and perhaps impossible for very large objects. Who the frell knows? But just because they didn't stop for a disertation does not mean they didn't have a plausible explanation. I think the demonstration that small objects have anti-grav and large objects don't fits fine with common sense film language physics.
* Maybe I missed it, but who said Earth was evacuated? I think G.Delight was right that there were more than one escape ship ... but I never got the notion that the ships held all 7 billion people on the planet. That's just dumb.
* And again, just because they didn't show the other ships meet with disaster or whatever happened to them whereever they are. Maybe there'll be a spin-off tv series about each of those.
* Similarly, even if the 7 billion skeletons haven't decomposed, not showing them doesn't mean they don't exist. It sorta makes sense (to me) that bio disposal would be one of the first jobs, completed over 600 years ago.
* Kevy already explained about the videotape.
* As for Eve's directive or capabilities, who's to say that the robots were not repurposed, or new ones built, or new programming done for new tasks, or robots - especially spacefaring ones - having many capabilities quite apart from fullfilling their prime directive.
* Yeah, Saturn's rings. Ya got me.
* Ok, very little oxygen on the Earth. Hopefully, all the humans asphyxiate 10 minutes after the end credits roll. Yeah, I got nothing for that one.
But Eve hardly conducted a massive planet-wide search. Perhaps there are plants in other zones, and seeds blew upon the stormy winds and were placed in the refrigerator by the ghosts of the decendents of Indiana Jones through his Mutt line of heirs.
And while there were no plants to form a food chain in Wall-E's city, perhaps there was an endless supply of twinkies to support a small clan of cockroaches.
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I'm sure I missed some of Alex's points, but my free time has expired.