1. The new iteration of the Matrix is set up to minimize the threat to the human batteries, whereas in the trilogy the integrated humans were dying by droves. All those cops and civilians in the originals, the randoms that agents cloned onto, were dead meat. In the new movie most or even all of them are just "bots." How did the Machines fail to conceive that design in the very first iteration of the Matrix?
2.The threat to the independent humans is also minimal, since the humans do not take to the field often, having doctrinally curtailed harvesting operations, and there is little expectation of any forthcoming attack on the human city, Io (IIRC), to the point where there is no evidence of the omnipresent militarization that characterized Zion.
3. Even the heroes plugging into the Matrix never seem to come very close to dying, and I'm fairly confident all of them make it to the end.
In the originals, of course, humans on missions died easily, and the threat of death IRL hung palpably over every moment a crew spent exploring the Matrix. As it happens, by the end of the third movie, almost every human character we had ever met was dead. It seems to me that not a single human died anywhere in the course of this entire new Matrix movie!