It doesn't matter if you're paying attention to Doctor Who or not, there will always be questions. In fact, the more attention you're paying, the more questions you'll have. Fortunately many of these can now be answered with 'Clara did it'.
In Genesis of the Daleks, how come it will take the Daleks a thousand years to get out of a short, broken corridor? Clara did it.
In The Two Doctors, why does the Chessene look out of the window when she hears a noise rather than, say, use her telepathy? Clara did it.
Why does Turlough always wear his school clothes even though the TARDIS has a full and expansive wardrobe and they must smell like a gym bag by now? Clara did it.
Actually, scratch that last one. That's just weird.
In order of how obvious the answer is to me, here are some questions from the Matt Smith era that have been playing on our mind. And hey, while we're all here, why not add some of your own in the comments! It might even be fun.
How exactly was Clara 'born to save the Doctor'?
A turn of phrase, or a clue to something else? Are we one day going to pan away from the shot of the leaf hitting Clara's Dad in the face, and see River Song underneath a tree with a pair of scissors? Or Rassilon, free from the Time War, spitting furiously and raising his Doom Gauntlet really, really slowly again?
Is there still an element of mystery to be revealed about Clara Oswald, or will she now be free to have some character development? Jenna Coleman hopes so, according to an interview with zap2it:
"We couldn't get to know too much about her because she was a mystery [in Series 7]. It's going to be nice just to have her as a human, as a girl. There's quite a lot to explore still, I think."
Coleman's done great work so far, so hopefully a new Doctor will shed some new light on his companion. Possibly someone to talk to regularly other than the Doctor might be a help.
What happened to Trenzalore?
At the end of The Time of the Doctor the survivors of Christmas on Trenzalore were left with a town to rebuild, as their protector finished regenerating and promptly buggered off (why, oh why do they always set the TARDIS in flight before regenerating? It never goes smoothly. Notice the Master in Utopia cunningly waits until he's finished before attempting to go somewhere).
By the end of The Time of the Doctor Trenzalore was not in the same condition as the planet we saw in The Name of the Doctor, lacking a huge graveyard and a giant looming police box. It's not confirmed explicitly, but either it's still out there in the Doctor's future, still his final resting place, or time has been rewritten.
Clara asked for time to be changed, and the Time Lords involvement certainly helps make that seem more plausible. Incidentally, if this is the case, changing the events of two episodes ago, it's not actually the quickest alteration of a timeline in Doctor Who; it's beaten by the alternate 1980 in Pyramids of Mars and the Master's reign of terror in The Last of the Time Lords.
What happened to the time machine from The Lodger and Day of the Moon?
In The Lodger the primitive time machine was described as having 'crashed some time ago', and the Silence faction in Day of the Moon have been influencing human history to, err, build a space suit (can't help but feel there must've been an easier way). While this remains unexplained, it also doesn't feel colossally important (it might well just be a crashed Silence ship), and might only be brought back if a writer thinks of a link.
Who was the woman in the shop who gave Clara the number to the TARDIS?
This one, from The Bells of St John, may well be resolved at the end of Clara's arc, but for now it's still hanging loose. Hell, maybe the woman in the shop was another Clara, and maybe the disguise she used contained traces of lead so she died again. Other options are River Song, Tasha Lem, and literally anyone else in the universe apart from Susan, Romana and the Rani.
Who is Tasha Lem?
Besides being the Mother Superious of the Papal Mainframe, she's probably River Song isn't she? There are too many similarities for it not to be (a very forward psychopath in a relationship with the Doctor), and it makes sense for her to be in the Eleventh Doctor's last episode somewhere, so it's probably River, QED.
Only then we have to ask where the Tasha Lem incarnation fits in to River or the Doctor's timeline.
Where might Tasha Lem fit into River's timeline?
We might not find out onscreen, though we don't know what happened to River between regenerating in Sixties New York and being Mels alongside her parents in Leadworth, so it probably happened there. However, this allows for the possiblity of Tasha regenerating, and she was meant to have died. If she is River, then she could occur after Silence in the Library/The Forests of the Dead. Churches do go in for resurrection, although not usually by extracting assassins from one of their breakaway sects from a computer in the future.
Steven Moffat has said that River won't be involved from now on except for story reasons, if someone comes up with something where her presence fits. However, Moffat lies. Obviously he does. Not only has he said so, but Doctor Who isn't even real. We've checked and everything.
Of course, the possibility exists that Tasha Lem is not River.
When does Tasha Lem fit into the Doctor's timeline?
I can imagine – though I have been told I have a sick and diseased mind – the Second Doctor sitting, arms folded, huge smile on his face, as she puts an arm around him while they're watching The Muppet Movie. Then nothing at all happens. Nothing. So don't imagine that. Or that. You disgust me.
If Tasha was a member of the Church when she met the Doctor, it's always possible that he forgot about the Silence, otherwise that would have been a bit of a clue. The Doctor could also have first met her after he knew about the Silence, during one of his offscreen travels. Then cheated on River with her, as the Eleventh Doctor's went from childlike awkwardness to randy teenager towards the end of his life.
You have to extrapolate a lot doing this. No wonder most people don't bother poking at story logic.
What happens if the Time Lords come back?
This is quite a big problem. As seen in The Time of the Doctor, if the Daleks get the slightest hint of the Time Lords' return they will mobilise in force/bring one really big flying saucer. So, assuming the Doctor does manage to sneak his people back into the universe through a back door, like an eighteen year old smuggling underage drinkers into a club, what's to stop someone shouting 'Let's do the Time War again' and all hell breaking loose?
We don't even know if the Time Lords have calmed down after the whole 'Being shoved into a pocket universe' thing, or if Rassilon's still planning on turning everyone into beings of pure thought, or if the Master's still about and turning into a big jumpy skellington. Presumably there have been lots of meetings, and that bloke who keeps saying 'Doctor...who?' is getting a sore throat.
There's only one solution to my mind: TIME LORD MINISODE PLEASE.