I think there's a distinct difference between 'complex' and 'complicated' when it comes to story writing. The former would be a successfully woven story that crafts everything satisfactorily together in the end, no matter what winding path it took to get there. The latter is a bit more of a mess which might have the makings of a wonderfully complex story, but it ultimately falls short because of plot holes, inaccuracies, or sometimes because it asks the viewer/reader to suspend belief a little too much.
Moffat's writing teeters on a frustrating knife edge between complex and complicated. Now and again it manages to work pure magic in terms of storytelling. But also quite often his writing leaves something to be desired as well. Some elements of his writing are wonderfully complex, and the ideas he explores are often stunning - totally appropriate for an ambitious show like Doctor Who. But sometimes he seems to hit a snag where not everything ties up nicely, or something is in contradiction to something else, and it's not nice to have to admit he does cave in to some of the common traits of very lazy writing;
"The Doctor lies" is a prime example. On the surface this could be an avenue to create a complex character out of The Doctor - trying to deduct some of his lies and make you genuinely think about the character. However Moffat's use of this idea is always explicitly stated when it's relevant, and it's not to make the character any more complex. Instead it's to get around a trap in his own writing, to advance the story he's telling now. There will often have been no indication that The Doctor was lying prior to the confession that he did.
As a viewer we're supposed to be more aware of the characters than the characters are, and Moffat neither allows us to be a lot of the time nor does he plant the seeds that allow more attentive viewers to figure these things out for themselves. 'The Doctor lies' becomes a get-out-of-jail-free card for Moffat and any other writer that decides they want to use it, and it over complicates things because the viewer will now need to keep up with individual scenes to keep continuity rather than watching it develop naturally. It is not in any way clever to suggest that your main protagonist lies as a means to resolve a plot against conflicting continuity, more so continuity that the very same writer imposed.
I absolutely love a good story arc, but it needs to be treated with care and done right. RTD nailed this more than once, by feeding subtle hints that don't detract from individual episodes but reward viewers who have stuck around the longest. On the other hand some of Moffat's episodes have submitted themselves to a story arc so intrinsic that you need to follow things a lot more attentively. That doesn't make the story any more complex or clever, that just makes it a whole lot more demanding. A more demanding storyline can only work when the pay off is satisfactory - if you fail at this, it makes viewing past episodes a far less enjoyable experience, as you have to waste so much time on a storyline you don't really care for.
When you end up resorting to ideas like 'The Doctor lies' when resolving some long-term unanswered questions it understandably doesn't satisfy as many people as a coherent explanation might have done. In fact it will frustrate many viewers who have stuck by the story and invested in it, only to be told that the characters knew more than they did all along. Doing it once well could be an interesting plot twist, but as a continuing motif it's both tiresome and lazy.
Perhaps not so much the fault of the writer, but the pacing of the story permitted by the episodes is also a major factor and this has knock-on effects. Series 6 suffered a lot from this - having over 90 minutes to introduce a series-spanning story arc, having the same again to give it depth in the middle of the series, and then less than 45 minutes to wrap it all up in a mediocre finale. That's the equivalent of making six Harry Potter films and then summing up the final book in a minisode. Doctor Who is never far off of that these days, bunging all manner of important and interesting content into mini-episodes. The proper episodes are no longer given any additional running time and while this isn't the fault of the writer, Moffat should all-the-same ensure the story he is telling can be adequately received by the viewer. I enjoy a lot of what he writes, but even my favourite episodes from him have major shortfalls and frustrating issues. He throws in what could be interesting, mature ideas regarding his characters - Baby Melody's kidnapping in Series 6, Amy's infertility in Series 7... but these are glossed over in the space of a single episode. True, Doctor Who should never be a domesticated soap opera but if Moffat isn't going to write these ideas into the show properly then I wish he'd not include them at all and spend more time explaining his plots in a satisfactory way. It's a matter of including the absolute best elements that suit a particular story, be that the best aliens for the episode, or the appropriate use of emotional gravitas. If The Time of the Doctor needs more time to explain the various plot threads in the air, then take out that Weeping Angel scene that added nothing apart from reminding us that they were there...again. If The Angels Take Manhattan is going for an emotional wallop at its end, give the scenes time to breathe rather than shifting the two longest-serving companions of NuWho in a third of the time Rose alone got at the end of Doomsday. If The Bells of Saint John is going to spend some time in Cumbria at its start, will it mean that time is wasted and the face-off against Miss Kizlet lasts only about sixty seconds? The writer should always be aware of what matters most in a story, and quite often I think Moffat completely loses focus. The Wedding of River Song had a constrained 45 minutes to wrap up the enduring arc of Series 6 but went off on a tangent to tell its own story complete with floating Mini Cooper's and Steam Trains in pyramids. The story went on slightly unresolved, whilst the main antagonist of the series was left in a state of limbo and we never found out what happened to her. The Time of the Doctor was so busy wrapping up plot threads that had been left dangling that it had to invent a brand new character from The Doctor's past in Tasha Lem, purely because time wasn't spared to bring back a former character we already knew or flesh out a whole new one - but we still had time for scenes of nakedness and angels. :where's that roll eyes emoticon when you need it?:
I love a lot of what Moffat writes, and when he gets it right he does it well. But unlike RTD he can't fall back on quite so endearing characters when the technicalities are brought into question. He can't single out many defining classics across his era because so many of his stories are wrapped up in his own ongoing saga of endless questions and few answers. A decent story has a beginning, middle and an end... there's no rule saying they have to be in that order, and it's inspiring that Moffat so adamantly wants to challenge that idea in a show rooted in time-travel. But the thing is that the end of the story never seems to have been in sight when it often should have been, and the overall impression made between some lazy ideas and some poor creative decisions is that Moffat has offered up something that is complicated, rather than complex.
