Hey MB, I'm going to borrow your list and your comments to expand my own thoughts.
9. River Knowing The Doctor's Name
If River never shows up again, we have to assume in the 100 years odd of married "bliss" Doctor and River had that he at some point told her, but in Silence in the Library we're lead to believe there's only "one time he ever could" tell her this information. Still... she is his wife.
And she very clearly says in Name of the Doctor that she spent a long time wearing him down to convince him to tell her. I don't think it's out of the realm of possibility to assume that we'll eventually see an 11/River Novel or Big Finish or even Comic Book series that slowly builds to this moment. The whole "11/River spend years having off-screen adventures" feels like insurance for future side stories to me.
8. The Duck Pond With No Ducks
Clearly this is the cracks doing. I'd assume that would be obvious.
Yes. This was not stated clearly, but it was stated. It's part of the Doctor's rant when he's figuring things out in Flesh and Stone.
7. The Clerics
I would like to find out the whole deal with the clerics, but I always assumed it was simply a semi-lazy political comment by Moffatt on the militarization of religion.
I always just figured it was world building.
6. The Silence
If Moffatt knows what he's doing, and I mean, that's the overall hope; The Silence will have something to do with 11's regeneration. Either that, or the Pandorica/Lake Silencio/Great Intelligence situations have proven them to be fucking idiots and they disbanded.
I kind of hope the Silence just quietly go away, but I really don't think it's likely. They were really good villains in Impossible Astronaut/Day of the Moon, but that's it.
I wouldn't mind Kovarian coming back, though. I liked her as a villain.
5. The Doctors Daughter
The episode was shithouse. Move on.
I think I'm the only person on earth who liked the Doctor's Daughter. I think given her own show and/or character arc where she's torn between her military programming and the Doctor's influcence could have made Jenny a compelling character. She even could have been a nice addon to Sarah Jane or Torchwood.
That being said, losing her wasn't a huge loss, either.
4. The Doctors Character Changes
That's called "character development" WhatCulture. A person who's been alive 1000+ years is bound to undergo some personality quirks, especially if you're not ignoring the fact that it's been stated multiple times the Doctors are all different men essentially with the same memories. Check your mythology.
Not to mention the toll that the Doctor's stressful life must take on his emotional state.
3. The Doctors Lie About The Gamma Forest
This was a simplistic throwaway thing to show how not everybody the Doctor touches can be an Amy Pond or a Rose Tyler, and people are bound to get hurt. This, in turn, contributing to the "Doctor = Warrior" shtick. Reading into things is fun, but too much.
I did always expect the story to swing around to having the Doctor visit the Gamma Forest. I honestly thought it would be in the slot occupied by Let's Kill Hitler. But they didn't do it, and that's OK. It'd be weird to go back now.
2. Is Series 7 Really Out Of Order?
Probably the only interesting idea in the article. I like the idea that the insistence on killing whatshisface in A Town Called Mercy is an effect of his hatred of the Angels. Probably doesn't hold much truth, but pretty cool. And the ending of TATM pretty much implies this sort of with him telling stories to Lil' Amelia.
If memory serves, The comment about the charger is in Town Called Mercy, while the actual scene is in Power of Three. But I believe Power of Three jumps around in time a fair amount. (It's been a while since I've seen it.) I think we're just seeing some of the events out of order, which kind of makes sense for the Doctor's life.
1. Jack Harkness Future
Again, a throwaway remnant of RTD's era that he left open for a future writer who was potentially interested in the idea. Moffatt clearly is not.
It was a funny gag, and that's about it.