I have a Theory of what will happen with Neo's remains and the struggle between Zion and the Machines to have them.
I think that the Machines will end up having more power than they could imagine when they plug Neo's body back into the system. So because of Neo's power, the Machines will say to Zion that they will let a lot more blue-pills to be released, because they no longer need their energy in the pods. So it will be a choice for Zion and Morpheus (who is not dead in my opinion) to want Neo's remains back and not release any more blue-pills OR to think that Neo's sacrifice happened for a reason and let him be plugged in to give the Machines enough power so that blue-pills will be saved.
So the problem is choice. Between the salvation of others or the remains of Neo.