In one sense, this is quite right - The Hobbit's structure amounts to a lot more than the idea of getting through "levels" (trolls, goblins, wargs, spiders) to reach an ultimate Boss-Level Baddy (Smaug). On the other hand, you can see how people who have learned about narrative through computer games might try to fit it to that template - and even be annoyed at the way it doesn't quite work ("Battle of the Five Armies and Moral Complexity wtf?"). Besides, one can't deny that Tolkien and computer games share an interest in quest structure, or that Tolkien has been directly influential on games designers, which may seem to invite the comparison.
This has got me to wondering more generally about the mutual influence of computer games, literature and television. The monster-of-the-week + Seaonal Big Bad structure was popularized on television by Buffy, I gather, though it crops up earlier - in Sailor Moon for example: was this an example of the Gameboy aesthetic filtering through to television? It now seems almost obligatory for some kinds of show - not least any that Steven Moffat is involved with. But the influence, if it exists, is on reading as much as on writing - and it feels like that structure could be read back into - well, not just The Hobbit but, say, most books of The Faerie Queene, the myth of Perseus, etc. etc., or any story where the protagonist overcomes a series of (perhaps increasingly tough) obstacles en route to the main encounter. In Bruce Lee's Game of Death the fights take place literally at different levels as he works his way up the pagoda: it's hard to believe it wasn't made with computer games in mind (though for reasons of chronology it clearly wasn't). Dante's Inferno seems equally ripe for pixellation.
In its purest form we'd have to see in the early adventures of the protagonist not just a kind of "training" or toughening up in preparation for the Big Battle at the end; those earlier antagonists ought in some sense agents of the Big Bad. So, just as Wario and Moriarty have a hand in many of encounters of Mario and Sherlock even when they're not on stage, so we might be inclined to expect, or demand, the same of Medusa, Smaug or Acrasia (and in Acrasia's case we wouldn't be disappointed).
Personally I love loose-jointed, picaresque plots as much as I like tightly constructed ones, and I'd hate it if anyone thought less of, say, Theseus's journey to Athens because Procrustes didn't turn out to be in the pay of Medea. I don't play many computer games these days, but a lot of them, from Animal Crossing to Grand Theft Auto, seem to be far more open-ended and exploratory than the Mario-style games of old. I wonder if this style of narrative will find its way into fiction and TV, and by what indirect crook'd ways?