First off, 8E disregarded the Storm of Chaos, moving the setting back before it. A rather good choice all things considering.

Second, the thing is you can't have Nagash return as he did without leading to the Incarnates as he tore loose Shyish, the Wind of Death, from the Vortex and bound it to Sylvania and later himself. The effects of that were pretty big on their own right. The Amethyst College exploded and most of its wizards were killed, the dead began to rise on their own, it killed, or at least greatly weakened, the Elf Goddess of the Dead, screwed around with at least the human underworld, weakened the Vortex and would enable Teclis to eventually free the other Winds to create the rest of the Incarnates.

Bottom line, Nagash is the second greatest threat to the world, second only to Chaos. Keeping him in a 9E is a mistake as having someone that big around means that he should be doing something fitting of his status as the Number Two Big Bad. In the End Times he was hamstrung by the fact that Teclis meddled in his plans, sacrificing his own niece to ensure the curse of their bloodline afflicted Nagash, forcing him to bind Shyish to Sylvania first and devour Usirian, the Nehekharan God of the Underworld, who might have also been Morr, and to send months in the Black Pyramid slowly binding Shyish to him. Before of course the Skaven showed up and destroyed a key component of the Black Pyramid, forcing him to abandon his plans and join the other Incarnates.

Even if you take away the rest of the End Times, Nagash is still an immensely powerful being and in control of Shyish and the human spirits of the dead. You can't really have a guy that power sitting around in Sylvania all day long. Eventually, even if his plans to become greater than the Chaos Gods is dashed, he's going to act.

And well... he's going to create a massive war, especially without any of the other Incarnates to oppose him. Like the Great War Against Chaos or the Sundering or the War of the Beard big. And given how he's tore out one of the Winds... well you have to do something with that. Either create the other seven Incarnates to counteract him or find a way to strip him of Shyish and restore it to the Vortex.