Alright Ill take these one at a time. But first let me make it clear, I haven't read all of the theories and backstory that some of you have. So if some of my answers seem uninformed it's because they are lol. I plan on going back and reading most of the top theories on /r/asoiaf and reading the sparknotes for the entire series. With that being said......
1 I think that this one makes too much sense not to be true. I agree with some that it almost too obvious for GRRM writing style, but I believe that is partially due to the fact that we have had ages to dissect the books. I think if everyone would have only had 2 years (haha yea right) between ADWD and WOW there might not be such concrete evidence. To the debate on here regarding Ned telling Cat, IMO there is no way in hell Ned did or would have told her. He was a very quiet private man who’s #1 character trait was honor and duty. If Lyanna told him not to tell anyone, Ned's lips where sealed. My own personal theory is that the reveal of Jon Snows lineage will be told through Bran's eyes, by him going back in time and watching.
2 I think the Jojen stuff is just a funny coincidence. I dont think the paste itself was made into a big enough deal at that time during the story for it to be a big reveal later on. So if that is what happened IMO we would have found out right then. Frankly without the theory popping up around the internet idk if I would have even remembered Bran eating the paste. I think Jojen is lost in one the the cript tunnel areas and the first challenge/test of Bran's new abilities in tWoW might be to find Jojens corpse.
3 I think most people will end up being disappointed by the remaining story concerning Benjen. I think he has already finished his primary use in the story. I think his purpose was simply to get Jon to the wall. Without Benjen there is no way to realistically turn Jon into a crow. I think we may see him later on during a battle, maybe Jon takes a moment before killing one white walker because it looks eerily familiar. Leaf blew up the Coldhands theory by saying that he has been around for a very long time. I don't see any way that Benjen is Darrio. The two characters personalities are completely different. Even if they where similar you still have to find some way for Benjen to make it around the wall and across the sea. There is also no plausible reason for him to know about Dany at that time.
4 Oooooh boy, this might be where I get kicked out of this thread lol. I personally really enjoy Danny's chapters. I think they show off possibly GRRM's greatest skill as a writer. That being his ability to craft such unique and distinctive voices for every character. With Danny he is giving us a perfect representation of how a teenage girl with a messed up backstory would react to be handed this amount of power. Sure she makes terrible decisions, is a huge hypocrite, makes impulsive decisions, and is partial to falling head over heals for guys, but those are all traits I would expect from a teenage girl. Throw in the fact that genetically she already should have a propensity for some mental instability and I think you see a character written very closely to my expectations of her at least.
5 I think the others created the wall. The structure itself is just to massive to have been made by man. I think for whatever reason the Citidel wants to wipe the record of the creation of the wall. That would explain the missing and incomplete history books that are all over the place. The passage about there not being any room in their world for magic (paraphrasing) is important IMO. The Citidel wants to wipe magic from the world and the creation of the wall might be the biggest example.
6 To be honest I didn't pay much attention to the prophesies as I was going through the books. I'll have to go back and brush up on the theories and such. But my guess would be Danny obviously, Jon, and Tyroin. But I could also see Bran warging a dragon, even though most people seem to believe Bloodraven was simply talking about ravens. I could also see it being Jaime instead of Tyrion based on the fact that Martin for whatever reason parleyed the meeting of Danny and Tyroin until the next book. Im not convinced it will even happen at this point.
I'll also run through a couple of topics quickly that caught my attention reading through the thread.
Favorite characters: Jon, Tyroin, Jaime, Stannis, Davos, and Mormont.
Characters I love to hate: Cersei, Mel, Ramsey, and Roose.
Characters I just legitimately hate: Brienne and Sam.
I don't think Margaery is white and pure. I don't buy for one second the excuse of her riding on a saddle a lot. The girl has gotten some D. I think especially the way HBO is portraying her you can tell she is playing the game. Also the whole moon tea thing is suspicions to me, it's a great plan if you can get Cersei to believe you asked for it and then use that against her. But the fact that Margaery actually did ask for it makes the issue of her needing it or not irrelevant. It's like trying to trick someone into thinking you robbed a bank, and to trick them you actually do go and rob a bank. At that point your motivations don't really matter. That is why im inclined to think Margaery actually needed the tea.
I don't mind changes from the books to the show. Honestly a lot from the books just wouldn't translate that well to screen. The combination on inter monologue and the story being written to stretch thousands of pages makes it a beast to translate. Most of the time they have gotten changes right, and even when I dont think it worked as well I can usually see where they where coming from. The one that always bothered me was not having Renly eating that peach during his meeting with Stannis. It was just such a weird visual and a small thing to add that I was bummed when it didn’t make it.
I think the stuff about Old Nan's tales is fascinating.
That's all I can think of right now, tear me apart lol.