Disclaimer!! These are peiced together from my own thoughts and opinions and those of others.
1. Weeping Angels are dead Time Lords.
If you are a Whovian the you know about the famous Weeping Angels. They made their first appearance back when David Tennant was the Doctor (in the episode Blink) and have repeatedly made themselves known. Now you may be asking "If the Angels are a species older then Time Lords then how could they be Time Lords?" Well here is the theory.
In the End of Time the leader of the Timelords states: "The vote is taken, only two stand against and will stand as monument to their shame: the Weeping Angels of old!" (36 minutes into End of Time part 2) And the two Timelords and standing, covering their eyes like the Weeping Angels.
So (now bear with me and imagine for a minute) what if a few Time Lord's traveled back in time, got stuck, and died. And hence, the angels. Or maybe there was a place that the Time Lord's got sent to as a punishment. That theory is supported by the passage above.
The Doctor also states in another episode that the Angels are "the only psychopaths to kill you nicely." Maybe that stems from their ancestry of being Time Lords who are known around the universe for being good?
It's also said in a episode "Lonely assassins, they were called. No-one knows where they came from. They're as old as the universe, or very nearly." So once again, they could be punished Time Lords. We will never really know.
2. The Master is The Doctors brother
Now I personally think that this theory is pretty far fetched, but after some researching I found some hidden clues.
Here are some commonly known facts about The Master. We know that The Master comes from Galifrey, as does The Doctor. We also know that The Master regenerates, as does The Doctor. But the big point I am going to make is that The Master and The Doctor really don't like each other. But why? What happened long ago to make these two people who are so much alike just simply hate each other.
Maybe, just maybe this dislike came from a long ago sibling rivalry. Now if they are siblings they wouldn't share the same dad. The Master (during his reincarnation Missy) mentions her father not our father. So maybe that is where the hate lies. It's possible that The Master and The Doctor share a mother. Maybe that mother cared more for The Doctor then The Master. If your mother loved your brother more, wouldn't you want some revenge.
And one more thing to back up this theory. The Doctor believed that The Master was dead (that is until Missy showed up). The Doctor stated that he had a brother...once. His brother was gone. The Master was dead. Coincidence? We may never know.
3. Why did the interface appear as Rose Tyler?
Now any self respecting Whovian knows of the epic love story of Rose and The Doctor. But in the end they couldn't be together. she got stuck with a version of him. Not the real him. We all thought that the Doctor would never find true love again. But then River Song popped up.
We first saw River in the episode Silence In The Library. she claimed that she was someone special to The Doctor. She whispered something to him that we all guess was his true name. And she had a sonic screwdriver. River finally became a constant companion once we met Matt Smith and we all grew to love her sass. River and The Doctor eventually get married. We were all overjoyed that he finally had the love he deserved from his devoted wife. But did he love her back?
Now I have no doubt that he didn't care for River to some extent. That is proved by the scene in the episode The Name of the Doctor when River reveals herself and the doctor said that it would hurt to much to acknowledge her before.
But here is what I am getting at. In the 50th anniversary speical The Day of The Doctor the War Doctor has a box that he will blow up to destroy Galifrey. The interface appears to him in the form of Rose Tyler (though she introduces herself as Bad Wolf). She tells him that she picked that form especially for him because it was someone very important from his future.
But why did the interface not appear as River? The answer is simple. The Doctor never got over losing Rose. He married River, leading her on to believe that he loves her, when really she was just a close friend. Maybe he believed that it would help. Apparently it didn't. And that hurt he was talking about was just the guilt from lying to her for so long.
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Your right! Time Lords and weeping angels are both aliens and how else would the doctor know exactly what they were the second he saw them?