Re: Which villain(s) should the reboot start with?
Regardless of the villain, I would prefer they not pursue the X (Villain) wants to destroy Gotham scenario. It has been overused, and there are seventy years' worth of better motivations to cull from. I think if they made the stakes personal - a la Skyfall - they could work wonders with the villain, such as Hush. If they pursued this route, I would prefer they cull from Heart of Hush, as his motivations in the original gn were not the best. Plus, with Hush, they could introduce more of the rogues' galley, without having to provide exhaustive backstories.
Outside of Hush? The Court of the Owls would be terrrific, or another secret society (I would save the Black Glove for several films down the line.) Plus, I would prefer they tailor the narrative towards the original Bond cycle: I do not want another trilogy, but, a series that can go on. If not societies, they could use a manipulative villain such as Strange or Riddler, and have smaller villains working with/for them (I really want to see Doctor Phosphorous, Cornelius Stirk, Deadshot, Maxie Zeus, Film Freak, and so on.)
The Joker would be great to introduce in the second or third film. If they introduce Harley Quinn, I would prefer they use the characterization from the Birds of Prey television show, and a costume based on the one she had from Arkham City. Or something Ledger-ish.
A gang war between Black Mask and Penguin would also be great.
Or, they could reintroduce Andrea Beaumont and incorporate elements of MOTP (at least she would exist in one continuity; I am very irritated that she does not exist in the comic continuity.)
In short, I would prefer they not use the "grounded" ratio present in the Nolan films. I love the trilogy - TDKR is one of my favorite films - but, I do not want the aesthetic carbon copied. It is time for some new blood, with a new take, to handle the franchise.
Batman vs Superman is an excellent film.