In an unguarded moment, a screenwriter once told me about the most dismaying Hollywood script conference he'd ever endured. It was a discussion about a project he'd been commissioned to develop by a major American studio: a lavish new movie version of Don Giovanni. An immortal story of love, sex and magic – with a great finale in which the anti-hero is dragged beneath the everlasting flames of Hell by the power of an enchanted statue. The screenwriter thought things were going swimmingly. The men in suits had laughed at his jokes. They'd appreciated the work he'd put into making the Don's career so marketably sexy. And the cheques they wrote in recognition of these efforts were paying for the education of his children. Then he noticed that one of the executives was sucking his teeth at something in the script. "This statue," said the executive. "Does it really have to move? And talk? I mean, it's a bit implausible, isn't it?" From this moment, the picture began to die a quiet but certain death.

Pixar, the digital animation studio founded under George Lucas in 1979 and bought by Disney in 2006, doesn't seem to employ people like that. Otherwise it would never have made the film it released on Friday: Up, a comedy about the aerial voyages of an obese boy scout, a talking dog, a giant bunch of candy-coloured helium balloons and an unlikely hero called Carl Fredricksen – a white-haired, square-jawed widower with a mouth like the slot in the front of a VCR machine and a trouser belt worn just below the nipples. The principal themes of Pete Docter's feature are the nature of bereavement and the poverty of materialism. Much of the action takes place in a clapboard house floating somewhere on the limits of the Earth's troposphere. And it's in 3D. Odd isn't quite the word.

Up is not the most left-field film in the Pixar catalogue. The studio's Ratatouille was the tale of a Parisian restaurant staffed by Michelin-starred vermin. Wall-E concerned the last inhabitant of a post-apocalyptic Earth, a robot that spent its days grubbing in the detritus of the absent human race and watching a tape of Michael Crawford belting out "Put on Your Sunday Clothes" from the 1969 film of Hello Dolly!. Imagine any of these plotlines being pitched to the panel of money guys in the Orange phone ads, and you'll appreciate Pixar's unusually high tolerance for creative eccentricity. As a policy, it has served them well. The virtue of employing hundreds of animators in the service of bizarre scenarios can be measured in millions at the box office, and the size of the firm's menagerie of Golden Lions and Silver Bears.

In a Hollywood enthralled to screenwriting gurus and their voodoo of jeopardy, character arcs, plot-beats, and the third-act reversal, Pixar's commitment to the whimsical and the peculiar is something to cherish. Acolytes of story-structure gurus such as Robert McKee tend to forget that familiarity has naturalised the essential strangeness of some of Hollywood's best-loved and most successful films. Close Encounters of the Third Kind, for instance, is about some aliens who make a date with a guy by compelling him to construct a model of their rendezvous point out of mashed potato. Douglas Sirk's classic 1950s melodrama Magnificent Obsession concludes with a romantic scene in which Rock Hudson trepans Jane Wyman's skull. Love Story, one of 1944's biggest hits at the British box office, stars Margaret Lockwood as a terminally ill concert pianist who, on a final holiday in Cornwall, falls in love with Stewart Granger, an ex-RAF molybdenum prospector who can't bring himself to tell her that he's going blind. And what is really happening in 2001: A Space Odyssey? Does the opening sequence have any logical connection with the rest of the picture, beyond the visual coincidence of a wheeling space station and a twirling bone hoicked by an angry hominid? Perhaps not, but then Stanley Kubrick never had to justify himself at a screenwriting seminar.

But it's the films we use to keep the kids quiet on a wet Sunday afternoon that are built upon the least likely narrative foundations. Old acquaintance with the sight of Judy Garland skipping about with a dog in a wicker basket discourages us from baulking at the plot of The Wizard of Oz, the story of a Kansas farm girl who is propelled by a tornado to a country where she helps a carnivorous mammal, some anthropomorphised straw and a collection of metal objects to acquire the best of human virtues. (The book, which Frank L Baum appears to have written with a tombola rather than a typewriter, is even crankier, and has the formal discipline of a dorm-room pillow fight.)

And would Walt Disney have made all those cartoon masterpieces if its plots, rather than being drawn from something reassuringly European and leatherbound, had been freshly minted by its authors during a pitching session? The one about the woman who lives in a secluded cottage with a gang of tiny bearded men who own a ruby mine? The one about the spiteful child carved from a block of wood, who smokes cigars and lives inside a whale? The oddness of Pinocchio exceeds anything dreamed up by Pixar. As one of those movie review sites for over-anxious parents notes, "Kids may be disturbed by Pleasure Island, where 'bad boys' are turned into donkeys and sent to work in salt mines." The disturbing thing is that, for the most part, kids are not remotely disturbed.

You have to go back to the 19th century to recover a moment when fiction for grown-ups was made with such strange materials. Readers did not grumble when they picked up Wilkie Collins's 1866 three-decker novel Armadale and discovered that it had two heroes, both called Alan Armadale. Nor were they fazed by the same author's 1872 novel Poor Miss Finch, which asked them to believe in a Sussex vicarage populated by a congenitally blind heroine, a silent child called Jicks, the widow of a Latin American revolutionary, a hairy-handed German oculist and a pair of twins called Nugent and Oscar Dubourg – the former a landscape painter and the latter an epileptic who has turned himself blue by drinking silver nitrate. Under the influence of modernism, which saw plot itself as a vulgar distraction from the higher business of symbol-wrangling and the communication of the ineluctable modality of being (or whatever), the novel fell out of love with such weirdness. Robert McKee's dicta on how to shape a movie plot into something tasteful and truthful share some of that austerity.

Up is not completely untethered. It still observes structures of desire and satisfaction. But the liberating extent of its oddness is revealed by the picture with which it will be sharing the multiplex over the next few weeks. Cloudy with a Chance of Meatballs is a 3D animated fantasy about a world in which food falls like hail from the heavens: rashers of bacon, doughnuts, eggs sunny side up. It's based on a picture book by Judi and Ron Barrett, in which this cascade of breakfast, lunch and dinner is offered as a quirk of nature in the town of Chewandswallow. But the film-makers clearly felt obliged to concoct causes for effects that the authors of the book were happy to stand back and enjoy. The movie's Science Bit relates how an amateur boffin develops a miraculous machine to "mutate" water molecules into food. The reckless beneficence of the gods has been rewritten as an act of overreaching by a cartoon Prometheus. Where the book has an occult wonder, the film has reason, logic and morality.

I suspect that studio executives put a far higher value on narrative logic and plausibility than the audiences that they're hoping to entertain. Every film version of Robinson Crusoe contains that heart-stopping scene from the book in which the castaway encounters a single footprint in the sand, and realises that he is not alone on his desert island. Today, Daniel Defoe would be laughed out of the conference room for suggesting it. How has Friday produced this solitary sign of his presence? Did he carefully scrape all the other footprints from the beach? Readers and audiences rarely bother themselves with the debate. Just as few will ask how many helium balloons it would really take for Carl Fredricksen's house to rise above the clouds. We all know that the idea is clearly as implausible as, say, a talking statue that punishes sex offenders by dragging them down to the underworld. And just as unlikely to produce a nagging point of order from the third row of the stalls.