They could have gone full Dark Knight and had:
- Kirk and Spock aggressively interrogate Khan where Uhura and Marcus were held.
- Have Khan try and start a war between the Federation and the Klingons using a psychological experiment.
- Khan corrupts the best Starfleet has to offer (basically the entire crew of the Enterprise)
- Khan betraying his Augments and being a lone wolf.
On paper, it already seems like a better story.
In all of Trek, emulating 24 really only worked for Enterprise, imo. Not just because they are close to 21st century humans, but because they don’t have a handbook as to what to do. They are the ones writing the handbook. So, the storytelling can be grey and have a bunch of ethical dilemmas that require pulling out the phase pistol first.