Why is Red Skull alive? To my understanding none of the other villain in the Marvel Universe trust him and we have two characters, Magneto and Dr. Doom, that hate his guts and both of them should be fully capable of killing him.
There are several possibilities:
They don't want to kill him because he helped them defeat the heroes.
They let bygones be bygones.
They have bigger problems then a megalomaniac with no powers like Red Skull.
Don't want to start a civil war between villains.
Or simply Red Skull is prepared for them and they know it.
My question is how can Absorbing Man and Magneto defeat Thor? Thor has beaten Absorbing Man before and Magneto has no other powers beside control over metal as far as I know.
Mags has control of the entire electromagnetic spectrum. That's one of the four fundamental forces. He's WAY more powerful than just "control over metal"
Absorbing Man is also a serious danger if he uses his powers right. In Earth X after developing his powers he became one of the most dangerous metahumans on the planet.
Seriously, Mysterio's mastery of special effects is second to none, but is it really credible that he could completely fool Wolverine's super senses to the degree that he would kill the ENTIRE X-Men team? Yes yes, berserker rage and all that, but Wolverine has extensive experience in people controlling him. Killing a few X-Men is very feasible, wiping them out to a man is stretching it. They should have given Mysterio some backup, maybe Loki popping in to add some extra omph.
The Mysterio in Old Man Logan isn't Quentin Beck, the first Mysterio and the one who was a special effects master. It's the third Mysterio - Francis Klum, who is a mutant and has abilities of teleportation, telepathy, and telekinesis and whom holds a large grudge against heroes.
Did Mark Miller forget the Hulk has a healing factor that might EXCEED Wolverine's? Nothing said during the story indicates the Hulk (or any aspect of his powers) has gotten any weaker; hell, based on Bruce Banner possessing super strength untransformed he might have gotten STRONGER. The Hulk probably couldn't WALK off being ripped apart from the inside out, but he should have been able to recover from it instead of it killing him.
It was canon for a long time that the closer to the surface the Hulk was in Banner the weaker he was. The smarter the Hulk was, the less Hulk like he became. With Banner having so much power untransformed and Hulk being cunning and calculating in his transformed state, it could be this Hulk is weak enough that his healing factor is suppressed (he certainly does not seem to have the top level strength the Hulk usually has). Obviously this has changed a lot over the years, but the explanation is there.
A lot of these Headscratchers can be weakly answered with "It's an alternate universe, so things are different."