To me, Doomsday would be the way to go if this were to be a "trilogy." But it would have to take place after the Justice League was established.
Superman saves the day from some threat (like Brainiac) but only finds out about the imprisoned monster. Killing Doomsday (or Darkseid, I really want him in there) ties the MOS saga full circle. The first film establishes that he's willing to kill if absolutely necessary, the second shows that he tries to find another way, and the third shows him understanding that what he did was neccesary in part one, but also shows him trying to control the collateral damage and save the civvies.
In other words, acts two and three absolve Superman of the guilt presented at the end of act one, in different ways.