I haven't read the rest of the thread, but I agree with anyone who thinks Missy is the Valeyard. I've broken down the reasoning behind my inevitably completely wrong theory below:-
1. She said she'd keep the Scottish accent, because she's expecting to become the (next) Doctor herself.
2. This is the producers sneaky way of seeing how people would react to a female Doctor. Clara's long winded angst/Matt's cameo gave the impression that they were nervous just about an older Doctor. This way the (sort of) Doctor is female, but if viewer reaction is negative, then she doesn't really count.
3. Some viewers seemed to think that her garden layout resembled the TARDIS console - anticipating her eventual home?
4. With Gallifrey back in existence, why would other Time-Lords be so interested in targeting the Doctor? He hasn't stumbled on a plan, which he's then foiled, he's being actively worked against. Weren't the Master's last actions pro-Doctor? Isn't he sane now? Maybe he misses the sound of the drums...
5. The Valeyard is trying to bring out the bad side of the Doctor - killing or causing the death of the clockwork chap is just a start. Maybe there'll be other such casualties over the weeks. We'll think it's just part of the new 'darker Doctor - how many people are already saying they like the fact that the Doctor might have killed? Missy wants to ensure that when he regenerates, he's such an unpleasant character, she comes into existence. Or something.
6. She passed the Doctor's number on to Clara in 'Bells' to ensure that she'd be on site to prevent the Great Intelligence rewriting the Doctor's life.
7. That's why the TARDIS sometimes seemed to not like Clara - because despite the fact that she saved the Doctor (you'd think the TARDIS would love her) she might somehow lead to the Doctor being 'replaced' by the Valeyard.
Even by my low standards of deduction, all of this is extremely unlikely, but I've had some wine...