"Why does the Question cause silence to fall?"
IIRC it's "The *answer* to the oldest question causes silence (The Silence?) to fall".
I hope/doubt Moffat will not answer this. Because that should be the Doctor's name, we are talking about and I don't think Moffat can know that name. Nobody can, hence, Silence (or…

If you are unclear about "fixed point in time" thing, I assume you have not seen the rest of NuWho for which that is relevant in relation to a recurring character. But it comes down to what you said, in terms of technical elements.
I guess this one could be chalked up to some often translated prophecy that changes…

"But River seems like she feels legitimately guilty over killing "the best man she ever knew". Saying "no, it turns out she was lying to everyone all along" feels like a weak kind of retcon."
It's ok that you feel that way, because it is a retcon. Back when we first meet her I didn't get the impression that she was…

I never got why RTD's Deus Ex Machina moments were supposed to be any worse than an entire giant season-spanning arc that makes no sense and is based on misdirection and plain acting of the characters involved.

Because the Flesh would die? While the Tessalator did just burn a little. Which nobody cared to check, I guess.

That's just two ideas that you can throw around and come up with explanations later on. Which is what this felt like, to be honest.

How much repercussion can it possibly have? We saw future events in the pilot and it looked like everyone but Victoria Grayson was celebrating Emily. Well, everyone left standing. I don't recall who was there or who is on this show, anyway. But most of them looked unsuspecting, to say the least.

Harper's Island comes pretty close. 
I was hoping this would be something similar, but that would make even less sense than the whole thing is making right now.

Esther might be not too great as a character, but I think Alexa Havins acted quite well in those scenes, switching from the procedural-exposition-mode to whiny-mode up to the scene in the van when she more or less did both at the same time. In the premiere I didn't think she could do anything besides the first mode.

Because I liked it and I still do. Certainly qualifies as guilty pleasure.

It seems pretty obvious to me that both Rex and Danes are anti-heroes multiplied by a thousand. I'm not sure if RTD is "serious" about it or if it's all some kind of extreme subversion of the trope. Possibly pseudo social commentary.

It was also referenced on the most recent episode of Eureka.