I think between writing D.o.t.D. story and T.o.f.D. story, Moffat had a new idea that contradicted something that was already filmed... and looked/sounded good for dramatic effect.
If he had already decided that Smith was the 13th, he wouldn't have included that line, or the glimps of Capaldi's eyes in DotD... as it makes no sense to include it. There was no need for it to be included, or quoted, as fans would have seen all the previous ones, and the story/plot would have been the same, without fans needing to see Capaldi as a teaser.

The thing that bugs me (now, even more than it did when I first whinged about it a few months back), is how Moffat suddenly had the Doctor age 300 years just to set up the plot device in DotD (to have enough time to do the calculations in his Sonic Screwdriver, and in his head) without him physically aging... and yet in this episode Moffat has the Doctor age 300 years (quoted in the episode) before Clara returns (stuck to the Tardis) and he is looking very aged.
So for one plot set-up of 300 years, Moffat doesn't make the Doctor age a day, but then a second plot device of 300 years, he's a withered old man who needed a walking stick.
Moffat doesn't make a good Editor, if he has to contradict himself as if it was the only option to resolve one plot device in DotD... and keeps retconning things, to the displeasure of fans who have now "lost" two regenerations. All those fan stories and theories of who the next two Doctors would be, not to mention the guidebooks, and web resources... all made useless in the space of two episodes.

As for the episode itself, it had some uncomfortable moments (unnecessary nudity plot device), and some funny bits (the Smith Doctor certainly likes making friends with former enemies)... and good wrap up of the Transalore plot device from N.o.t.D. but the timing of the story felt clumsy.
And just like the Pandorica episode, we have all these warring races together at one time and space, when most existed at differing time-periods to each other (based on when the Doctor has defeated or seemingly eradicated them). And again with the endless Daleks - they seem to be like a virus, that keeps coming back no matter how much it looks like the new Series has destroyed them.

He's also put way too much emphasis on the Time Lords being a dangerous race... as in, it is in the best interest of the universe that they remain lost, even though the Daleks are taking over, and the Time Lords are the only ones who could possibly stop them.
Bring them back, and if they really have the power of time, then prevent the Kaleds becoming Daleks in the first place (like the 4th Doctor was supposed to have done).

And one last fan-rant if a Time Lord can cause that much devastation when regenerating (according to the new Series), then why wouldn't it be used as a weapon against the Daleks. A couple Time Lords could destroy the whole fleet by sacrificing a couple of their regenerations. (and if the rest of them have the power to restart a Life-Cycle, they could just get a recharge later)
So many holes for this poor tragic fanboy...