These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Author's Saving Throw - Fantastic Four 2099 was supposed to star the actual Fantastic Four, briefly brought to the year 2099 by accident and trying to find their way home/save the world. It ended with The Thing getting killed in a shuttle accident, and the rest of the team promptly forgetting he ever existed and going home without him.Manifest Destiny gave a different explanation: the team was actually Artificial Humans created by the Watcher, because he thought his old allies would be able to help save the dying Earth. All four are brought back into existence in the end.
Complete Monster: Of all the corporate leaders in this universe, John Herod is easily the worst. After Doctor Doom conquers America and limits the power of the corporations, the corporate leaders turn to John Herod to kill Doom and return them to the old the status quo. Herod comes up with a counter offer: He will kill Doom for them, but only if they make him their leader. Herod also wants to strip mine the Earth and have all the corporate leaders relocate to Mars within 5 years, leaving the Earth an empty barren husk. When even the other corporate leaders balk at this plan, Herod threatens to kill them if they do not go along. Herod then launches a devastating campaign against Doom and his government. He attacks the White House and destroys Doom's floating city, Libera Cielo. However Herod truly crosses the Moral Event Horizon, when he kills everyone in Latveria with chemical weapons and sends a video tape of the Latverians dying to Doom, just to rub salt in Doom's wounds. Once Herod takes power, he takes measures to kill most of the remaining superheroes.
With a hint of irony. During his early Spider-Man works, Spider-Man 2099 writer Peter David "revealed" that Ned Leeds was the original Hobgoblin—which several fans thought was questionable given how Leeds died and the original Hobgoblin mystery writer, Roger Stern, came back and revealed that it wasn't the case. David had intended Father Jennifer to be the (Green) Goblin 2099, but it was revealed that Gabriel O'Hara was Goblin 2099 (though this was later retconned to be an imposter). Someone had to appreciate the irony, even if (as the link shows) David himself doesn't.
As "One Nation Under Doom" drew to a close, Herod created a Captain America clone as a puppet with the cover story that history had repeated itself and Steve Rogers was frozen in ice and revived yet again. Manifest Destiny reveals the fate of the real Steve Rogers; as it turns out, history really did repeat itself...