Oh I love the show so stinkin' much. It's the only show I actually try to watch live, even though that gets a bit tricky sometimes. I do think it's confusing, but I'm not all that brilliant so it's not hard to get me confused.
Dude, as far as the Zygons go, people are getting mad at the idea that tennant will be playing the alien disguised as the doctor. BUT, I read that to take on the form of someone, the Zygons' have to have that lifeform alive, sooo he'd still be alive somewhere.
"I think the Silence is going to somehow wipe The Doctor’s memories and one of the biggest memories they will try to wipe is his identity. (The Doctor was starting to do this before, WITH THE HELP OF OSWIN) but now it might get extremely dangerous for him.
The Doctor’s greatest ability and power against anyone of these species is that he knows who he is. EVEN IF THEY DONT. He knows who he is, what he can do, the dangers he’s been through, the losses, and how to defeat them. His greatest power is his identity. With out it…he becomes powerless.
Now onto Clara, someway these different Clara’s were created, mirrored through different places in time. I think she’s been sent as a key to help the Doctor remember (AND NEVER FORGET) who he is and what he can do. Sent by….we don’t know… BUT all these could be in order to save him for when he does meet up in his time stream and face WHATEVER is waiting for him in that field.
When we hear the quote “Silence will fall when the question is asked†we sometimes think the literal term “silence†as in quiet or END. But what if this is really the end of The Silence religious order? All by the help of Clara Oswin Oswald. She will be the girl who makes him remember.
This mystery of Clara will keep The Doctor intrigued. Keep him involved at his job and about who he is. As you can see, Clara isn’t in this field with him and I believe its because The Doctor has to face this alone WITHOUT the help of his companions. He’s been running from this his whole life and now he must face it.
She keeps repeating “Run you Clever boy and REMEMBER†she’s trying to help him never forget her but also keep his memories intact. So that the oldest question, hidden in plain sight, when its time for him to face it WONT be the Doctor’s end but it will be his victory."
^The above is not my theory, it's from someone on tumblr, but it's one of my favorite ones.