They should have never killed off Shane. Just have him seem to have been killed and or missing.
He would have been the perfect overriding arch enemy ever lurking in the shadows, scheming in seclusion , and occasionally throwing monkey wrenches at the group without the group knowing who's the culprit. And after Lori died, his character could have really gone off the deep end with an overriding madness to get his child back and going from harassing the group to bent on completely destroying the group in sadistic and twisted ways that would make the Governor blush. After all the worst enemies are usually the ones who truly know you and then betray you.