Actually, many call the version we play in "Ver 4.0" because the cycle of the anomaly is over, and those that choose to be free may do so.
But that's an entirely different debate
I think you're looking at this the other way around. Neo came about because something bad was happening, not the other way around. If he comes back he won't bring destruction, he'll be here because destruction has already come.
Neo came after the Matrix was created, the Matrix didn't come after. Catch my drift?
He does what he does because he has something to do it against. (It's late and I can't seem to get this point across.)
For example, when the machines were destroying Zion, he came and saved the day because there was a purpose for him to save the day. He stopped the war because we were about to be destroyed by something that already existed.
So, when/if he comes back, it will be against something that already exists so that he will have a purpose. He won't bring trouble, trouble will already be here.
Point 2. Proof of Neo's ability being personal, not code. HE GOD-MODE'D MACHINES IN THE REAL. End of story.
The topic of this discussion is not about the ingame return of Neo. I'll concede outright that the logistics of bringing him back ingame would be a detriment unless they can find a way around it.
But the topic of the discussion is seen as an "In Universe" discussion.