The superhero film gets stronger, while art house film-makers decry the lack of big-screen directing opportunities. It is a sad state of affairs when new movies from directors of the calibre of Steven Soderbergh and David Lynch may never again be seen in multiplexes, especially when those film-makers have made more than their fair share of notable contributions to the genres this column celebrates.

If there is a silver lining, it is that studios are getting better at making these preposterously expensive, spectacle-heavy movies. And they have become considerably more canny when it comes to recruiting film-makers to oversee them. The McGs and Brett Ratners of this world may still be in business, but executives these days often opt for directors whom critics are less likely to unceremoniously monster: hence, Guillermo del Toro's Pacific Rim, James Mangold's The Wolverine and Gavin Hood's Ender's Game in 2013. All of these are flawed movies, and none of them makes this year's top five, but all benefited from a little extra crackle and zing brought to them by film-makers with passion for the form.

I also enjoyed Peter Jackson's superior fantasy sequel The Hobbit: The Desolation of Smaug, which would have crept into a top six, and I loved Edgar Wright's The World's End for somehow managing to transform leaden memories of early-90s Friday nights round a pool table into shining comedy sci-fi gold. An honourable mention must go to World War Z, the troubled Brad Pitt post-apocalyptic actioner which emerged as decent blockbuster fare after an incredibly expensive last-minute reshoot. Joseph Kosinski's Oblivion was worth the price of admission for its marriage of M83's gorgeous soundtrack and Claudio Miranda's sweeping, peerless cinematography – it's just a pity the story and cast weren't up to much.

In a year when science fiction seemed to be ubiquitous – if you hate the genre, bad luck; it's going to get even worse once the new Star Wars arrives – The Hunger Games: Catching Fire ticked all the right dystopian boxes without ever really bursting into flames. There was also terrible space guff such as M Night Shyamalan's horrid Will and Jaden Smith vehicle After Earth, which only served to prove that Scientology on the big screen is still a Very Bad Idea more than a decade on from the execrable debacle that was Battlefield Earth.

A quick note to remind everyone that this is my personal top five drawn from science fiction, fantasy and comic book releases (the areas covered regularly in this column) over the past 12 months. For the Guardian's top movies of 2013, look here. My favourites follow, in reverse order.

Neill Blomkamp's latest venture into the future gave us a genuinely enthralling tale of haves and have-nots – a genre take on Captain Phillips, if you will. But where Paul Greengrass's Oscar-tipped drama posits everyman Tom Hanks as the victim of nasty Somalian pirates, Blomkamp makes Hollywood hero Matt Damon the downtrodden victim of mean old one-percenters who won't share their riches with the rest of the world. It asks the viewer to empathise with the desperate immigrant vying to escape poverty for the sniff of a chance of a new life among the privileged few, and points out the indecency of a society that refuses to share the fruits of its wealth with others. In Captain Phillips, Hanks' military rescuers are welcome heroes; in Elysium the defenders of the titular paradise above the clouds are stereotypes of cruel villainy. Blomkamp's film, like the best science fiction, uses futuristic satire to make us think again about our own society. It also lumps in exoskeleton power-suit battles and bazooka-wielding bad guys for good measure, thereby emerging as the most intelligent example of utterly brainless action since Starship Troopers.

Despite the risk of it turning out to be a confusing hotchpotch of well-trodden ideas, Cloud Atlas emerged as a film to singe the synapses and serenade the senses through the virtuoso directing and sheer unfettered confidence of Tom Tykwer and the Wachowski siblings. Wildly and unapologetically left-field, it was glued together via heartfelt performances from the likes of Ben Whishaw, Tom Hanks and Halle Berry. This was an enthrallingly elliptical movie that rewarded repeat viewings tenfold. It will surely come to sit alongside films such as Terry Gilliam's Brazil and Twelve Monkeys in the grand pantheon of nebulous fantasy, and one can only hope the film-makers vie to repeat the feat. A trailer for the Wachowkis' next film, Jupiter Ascending, seems to lean more towards a rather far-out take on The Matrix, but here's hoping.

Sure, it had screenwriter Damon "plot hole" Lindelof's influence all over it, but the sequel to 2009's Star Trek reboot had so much else going for it. From beautifully crafted views over 23rd-century London to the gorgeous opening chase through an apocalypse-threatened planet covered in blood-red foliage, here was a supercharged space spectacle to die for (though hardcore Trekkies may not have agreed). The key dynamic remained the wickedly bromantic chemistry between Chris Pine's risk-taking Kirk and Zachary Quinto's steadfastly logical Spock, but this time the duo had a pair of villains who were more than worthy of them. Benedict Cumberbatch's Khan might have added the touch of posh-boy Brit class that made the film, but the inclusion of genre hero Peter Weller added just the right touch of B-movie brilliance. JJ Abrams may be moving on to rival series Star Wars, but he has left the saga in very good shape indeed.

Fans of Robert Downey Jr's take on Tony Stark might have been a little concerned when Shane Black replaced Jon Favreau for the third instalment of the Marvel superhero series. They need not have worried, for the Kiss Kiss Bang Bang director proved the perfect partner to take Iron Man into the stratosphere at a point when other comic book sagas have traditionally taken a nosedive. The key was a genuinely baffling curveball of a plot twist involving Ben Kingsley's superb Mandarin that wrenched audiences out of their comfort zones via the kind of filmic sleight of hand rarely seen in mainstream fare. Stark (and Downey Jr) are set to return in 2015's Avengers sequel, but Iron Man 3 ensured there will be plenty of clamour for the character to make at least one more solo outing.

The joy of Alfonso Cuarón's 3D space thriller was that it married futuristic thrills to old-school movie craft in a manner perhaps not seen since Alfred Hitchcock's Dial M for Murder. Gravity may have ridden an early wave of success on the back of its arthouse leanings, but this was a good old-fashioned nailbiter that, with its penchant for lovably schlocky dialogue and unashamedly B-moviesque thrills, was always going to appeal to mass audiences. Together with last year's Life of Pi, Cuarón's gorgeous two-hander also helped convince critics and filmgoers that 3D isn't completely useless at a troubled time for the format. Oscar recognition could yet lie in wait, and surely few could begrudge the Mexican film-maker his time in the spotlight after his movie battled through a terrible extended gestation to eventual box office and critical glory.