Re: The Reboot Joker
He shouldn't be in the first reboot they do. Assuming these movies have at least three year turnaround, if they do the reboot in 2016, that means over ten years will have passed since Ledger's turn when they release a sequel. I think that will be quite long enough for the public's consciousness to be "ready" for a different version of the Joker.
I'm in favor of no "origin" per se, though I think some adaptation of Batman's first encounter with the Joker should be done--perhaps something similar to The Man Who Laughs (which I guess is now not the FIRST encounter, according to the New 52, which I guess keeps Batman #1 in continuity as well, but anyway, you know what I mean, one of the first encounters).
Not sure about Harley Quinn. Depends on how "wacky" this version of the Joker is--if it's a "lighter" Joker more in line with most of the comics or The Animated Series then fine.
As for how dark...I dunno, I reread the Laughing Fish recently. I liked that version. That's not very "dark" but definitely insane and deadly.
I actually have no problem with "make-up" Joker versus bleached Joker. I think it changes the exact nature of his madness if it's make-up, though. I assume they will be more comic-book-like with this new one though so they will probably go with bleached.
Relationship with Batman, I think at the end of the day there needs to be a deep-seated hatred of Batman that is simmering WAY below the surface. The Joker pretends he wants to play with Batman but in the end really would like to kill him--and is continually prevented from achieving this goal.
The only way I'd like Death in the Family is if it led to Under the Red Hood. Otherwise leave Todd out of it entirely. If you want to do Robin do an adaptation of The Long Halloween and then Dark Victory...