As this year's series of Doctor Who approaches its climax, so does this year's backlash. Following initial complaints that the series was getting "too scary", there is a new criticism: that the series' story arc has become too complicated.

Although series 32 arguably remains at its heart an anthology show of self-contained adventures, the cat's cradle of River Song and the Doctor's march towards his own death has started to alienate some viewers. For those not keeping up, we have so far seen the Doctor killed off – only to arrive back 200 years younger. He then spent weeks monitoring Amy's phantom pregnancy, until the pregnancy was revealed to be real and Amy an avatar. The baby was revealed to be River, who was conceived in the time vortex, and kidnapped and groomed as a Time Lord assassin to kill the Doctor. Maybe.

Things came to a head last month with Let's Kill Hitler, an exhilarating half-season opener that made little sense if you hadn't been following the story for the past four years. As commenter JimBow1 said in a hardly lone voice: "Far too convoluted. So is River the love child of Rory, the Doctor or the Tardis? So how many times is the Doctor going to be killed? Is he going to be regenerated as a cat? Where was the proverbial sink?"

Does this matter? Russell T Davies once quoted audience research that only about 10% of Doctor Who viewers were watching every single week. His successor Steven Moffat broke from that logic, announcing the longer story arcs saying: "It's time we stopped pretending that people don't watch the show." Moffat has also remained defiant about viewing figures – expressing some frustration that the show's high iPlayer numbers are not taken into consideration by critics who say that ratings are down.

But the show was beaten by Family Fortunes on overnight ratings last week. Which has inevitably led to the suggestion that Moffat's puzzle-box plotting has been driven people away. And while some fans of the show embrace the complex plotting, others think the series is in need of more standalone episodes and fewer twists in an overarching plot that has become unnecessarily complicated.

Gareth Roberts, the writer of three episodes, including Closing Time, which broadcasts this Saturday, is bullish about accusations of overcomplication. "I keep thinking of the pompous character in the Pet Shop Boys song Yesterday When I Was Mad: 'I enjoyed it though of course no one understood a word of what was going on …'," he says. "I would only be worried if Doctor Who was complex in a technical, scientific way – if it was all about 'reconfiguring the thermalobes'. This is emotionally complex, a bit like that thing … er, what is it … oh yeah, life."

Toby Whithouse wrote last week's episode The God Complex – considered by commenters on our blog to be a series highlight – as well as creating Being Human. He says: "I don't think the problem is that Doctor Who has become more complicated, surely it's the fact that the rest of television has become more simplistic. The themes and plots of (as the fans call it) New Who are no more complex than some classic Who stories. The only difference is, Tom Baker's Doctor wasn't jostling in the schedules against Red Or Black."

The God Complex was one of this year's more challenging episodes, and Whithouse concurs: "Personally, I think Doctor Who should be complicated. Not despite but because it's a children's show. It's fantastic that the next generation of storytellers are being told such rich and dark and intricate stories. When did having to concentrate become mutually exclusive to enjoyment?"

Roberts and Whithouse are, of course, two of Moffat's most trusted lieutenants, and arguably wouldn't criticise the status quo in public even if they wanted to. But reader Kathy Ball, mother to two children of 11 and 14 who have been raised on Who since the 2005 relaunch, would agree with them. "This series has definitely been more complicated in the amount of detail and cross-referencing, but in our house it's the parents who struggle, not the kids," she says. "I think it's because kids still have no boundaries to their imagination or thinking – they question but are still able to free their minds for all manner of absurdity. Plus, they have been nurtured on Harry Potter so outlandish plots and characters are second nature."

Indeed, it was Douglas Adams who said, as a script editor in 1979, that the challenge of Doctor Who was to make it simple enough for adults and complicated enough for children. In fact, none of the worry about complexity is new. In the 60s, The Daleks' Master Plan played out one story over 12 episodes, The War Games over 10. In the 70s, the series dubbed The Key To Time and the loosely connected E Space Trilogy spun arcs similar to that of River this year. The less said about The Trial of a Timelord from 1986 the better, but even after that, Sylvester McCoy's doomed-yet-improving tenure was playing out stories with Sophie Aldred's Ace that never got the chance to be finished.

Looking at the comments on our blog, the Marmite nature of series 32 seems more about whether you love or hate Alex Kingston's camp portrayal of River. But as Toby Whithouse argues: "The fact is, most people like the show the way it is. They can follow the stories, and week after week they are spooked and thrilled and delighted. The only problem with content majorities, is they tend to be silent." Agree? Let us know what you think below.

• We said that overnight ratings for the show were falling when we first published this blog, due to an editing error. In fact the story we link to shows only that Doctor Who lost out to Family Fortunes. This has now been corrected.