Nerdpants, activate!
I think they already destroyed the best possible application of Doomsday (who if you don't know, is the living alien weapon of destruction that ultimately sort-of killed Superman), and here's why.
The real impact of Doomsday, and indeed the whole Doomsday story, revolved around his unrelenting destruction of everything in sight. He is tearing through town after town, city after city. Massive destruction unlike anything that comics had EVER seen before. Superheroes are literally throwing themselves in front of him, just trying to stop that onslaught, including Superman, and it's all for nothing.
The trouble is, we've already seen that level of destruction. That's what we saw in Man of Steel. Leveling whole buildings, killing thousands, armies left in pieces, etc. What's worse is that, at least on the surface, nobody seemed to care about that destruction, or at least the human reaction wasn't a focus.
Right now, a Doomsday as written in the comics would just be more of the same. Ho hum.
A brief aside, I think an interesting take on Doomsday is what we saw in the last story arc before the New 52 reset: Flashpoint. Doomsday was the same alien force of destruction, but had been discovered by and was being controlled by the military (and Luthor, I think... I forget). Of course, that all goes wrong, etc. etc.