I wonder if the Flashpoint-New52 reasoning of "preparing the DCU for a terrible threat" still holds? Been a long while so my memory might be wrong, but......Pandora combined Vertigo, WildStorm, and DC because the DCU wasn't "tough" enough to handle a vague, oncoming threat right? Then in the Rebirth special, we find out that Pandora has been working for Manhattan (right before he destroys her) which would indicate that he's actually trying to accomplish something good (even though his methods aren't). Is that all correct?
We know suspect/know that Manhattan removed the JSA and killed the Kents. If he's trying to save the universe/multiverse, why would he do that? Because he's trying to harden the DCU and make the heroes more brutal, of course. Vertigo and WildStorm are full of hardcore badasses who won't blink at hard choices and body counts. The JSA are the elder statesmen of the DCU and their opinions carry weight; but they're old fashioned and not likely to support a tougher style of heroism. And way back in the New52, the death of the Kents was said to be a big part in Superman's rougher, more brash attitude (that he quickly outgrew, but still). So I still think Manhattan isn't the villain; he's still a misguided hero trying to do the right thing but unable to recognize the horror of his own actions, and we'll see the Watchmen and the DCU team up to battle this still unknown threat that Manhattan has been acting against.
However, with all the changes to management there's no telling what the plan is anymore.