If they have to revisit a classic episode, I think The Doomsday Machine being involved somehow could make for a great story. You'd have to change it up pretty good from the original, maybe involve the Klingons or another race that discovered it and is using it for its own ends.
This is what I think they'll do next.
Star Trek 3 will find our heroes in year 3 or 4 of the Five Year Mission--when they receive an urgent message from Starfleet Command. Rumors are the Klingons, with Praxis having exploded and panic about the Khan Incident still pervading the Empire, are looking for any advantage in the upcoming war with the Federation.
A Klingon commander named KOR is in charge of a Klingon expedition to find a rumored "Doomsday Machine" which the Empire hopes will act as a counter to the Federation. The Klingons are convinced that Starfleet has access to the superhumans like Khan as well as the Red Matter from the first film.
KOR won't be a mustache twirling bad guy. Instead he'll be a man on a mission for his Empire, determined to beat the Federation and ensure military superiority for a Klingon Empire besieged by potential threats from Starfleet, the Romulans, etc.
At least that's how I'd do it. But we shall see.