If the movie isn't going to feature the traditional villain type, then Trelane, the Horta, Mudd, and the Talosians all fit the bill, because they weren't really villains in a TWOK, Borg, or ST09 sense.
-- Trelane was just a misunderstood child playing out a fantasy.
-- The Horta were actually peaceful, but were forced into killing to defend themselves.
-- Mudd is just a guy who works in the gray areas of the law, sometimes getting caught on the wrong side of it.
-- The Talosians were actually trying to help Pike in "The Menagerie."
-- Gary Mitchell became villainous by accident.
Any one of them could create a conflict or some other type of problem for our heroes to resolve.
The problem is, regardless of who it is, we already know they aren't all bad. So, what twist would give it any freshness or create any new suspense? That's my question.
They did say they wanted to be topical. Oh! I know! Maybe it's Mudd. He was meddling in sub-prime mortgages on some planet and caused their housing market to collapse. The ripple effect threw the planet into a recession that now threatens to engulf the entire Federation. Millions of foreclosures. Millions of people under water. New colony construction grinds to a halt. The horror! The horror!