The problem with OMD-Peter gone Emo is that Kindred was involved with Mysterio's resurrection in David's FNSM which happened before the deal. So timeline doesn't fit. And as with Uncle Ben, do we really want the Spider-Man of AF#15 transformed into a vengeful murderer and torturer?
Ezekiel fits, Best of Enemies Harry fits, Gwen Stacy fits timeline-wise. All three were dead, all three knew Mary Jane (Ezekiel had dinner with them after all). Two of them are directly connected to Norman Osborn, while one you can imagine as being connected through business ties (Ezekiel).
From storytelling impact and suspense perspective, I think it has to be Gwen Stacy. Ezekiel is a surprise but also a character readers won't know and would have to be prepped up on (the same way Roderick Kingsley made appearances in ASM and satellites before Stern's Hobgoblin Lives to make it less of "oh-yeah-that-guy-from-that-thing-with-the-thing"). OG Harry Osborn would raise issues about who's the Harry Osborn running around, and would also negate the little growth Harry had in that time (such as changing his name to Harry Lyman and all) and likewise, we haven't seen Harry in Spencer's run, so even if he was Kindred no emotional stakes are sold to us about "the Harry we know and liked isn't Harry" and so on.
So it has to be Gwen. You don't need much to refer to Gwen. It's an instant hook. You can also make Gwen into a vengeful villain without really changing or ruining a character significantly. If anything her becoming a villain is consistent to the character in the page when she was alive. It would lend poignancy to that. And as anyone who has seen Mask of the Phantasm can tell you, it wouldn't be the first time a mystery villain paraded with a dude's voice and was addressed as "He" to turn out to be a dame.