I wonder if they had any idea of the arc's endgame when they started the whole Missy thing of if they wrote themselves into a box and had to cobble together something to resolve it...
Nah, it sure seems like he made it up as he went along. I also doubt whether he knew who "the girl in the shop" was when he first wrote that. There seemed to be no apparent importance for choosing Clara. None of the people saved earlier in the season were actually used in the finale. And, yeah, using the more primitive clockwork robots seems pointless. And, their pursuit of the promised land was lost along the way.
Mr Awe
Given that more than two years have passed since Clara's first appearance in
Asylum of the Daleks, it's safe to assume that Moffat may have had to change his plan a few times after already starting. Actually, it would explain a lot about the Moffat era. I haven't rewatched much of Season 5+ much, but where I do I'm struck retroactively by how different the start of an arc can be to the end of it.
Probably the reason that Series 6, 7 and 8 have received such criticism compared to Series 5 is that the latter was fairly-self contained, on time, and stuck to the RTD-era formula for the most part. It had a ten-story plan whereby the mystery built up for 11 episodes and was resolved in the finale. Series 6 tried to build on this, but seemed to fall off a cliff midway through with all the stuff about Amy's baby and lead to an ending (
The Wedding of River Song) that was just a mess.
For Series 7, Moffat clearly got into a pickle with Karen & Arthur's resignation, then Matt's and of course the Golden Anniversary. The divorce arc of episodes 1-5 strongly feels like a stopgap measure to have
something which could hold together what would otherwise be an odd string of unconnected stories jammed between two big arcs. 6-13 then feel like a full Season compressed into eight episodes with a rush to have some kind of grand finale that can be wrapped up before the 50th so that
The Day of the Doctor could be kept separate from rest of it and not get bogged down by any Trenzalore or Great Intelligence stuff (there are a few lines about Clara but they could be cut and it would make no difference).
The Time of the Doctor feels like a mid-season 6 episode two years too late, frantically tying up loose ends dating back to 2010 with single sentence hand waves.
Season 8 was better, but this episode definitely felt like some of it was rewritten at the last minute and not thought through.