The Zygon b-plot is indeed the weakest thing about that episode, and I agree that it would have been nice to get a resolution. I think Moffat didn't want to bog things down, and I understand that, but we could have gotten a brief shot of the Zygons leaving or something, just to confirm that it happened. But for me, that's a nitpick I can easily overlook.

I'm hoping someone will eventually write missing adventure fics for the War Doctor

I would definitely like more on the War Doctor! He's a great character. In fact, I'm kind of sorry they regenerated him right away, because I want some space for post-Moment fanfic with him. Oh well, I suppose it can still be snuck in -- with fanfic, there's always a way!