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.
This is finally answered in the Old Man Logan ongoing: Hulk snapped during the battle, and killed the (presumably already weakened) Thor.
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.
Mysterio lampshades that the other X-Men were holding back and not understanding how far gone Wolverine was, making them sitting ducks for him.
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.
What I don't get is how you're supposed to eat Wolverine in the first place. Adamantium skeleton anyone?
A lot of these Headscratchers can be weakly answered with "It's an alternate universe, so things are different."
How the hell did Red Skull survive but Loki didn't?
Ragnarok is the most likely explanation. According to the legend, Loki and Heimdall kill each other.
Shouldn't it take something like two hundred years or more for Logan's body to physically age that far? How is Hawkeye not dead of old age yet, along with other non-superpowered people? Was there some unmentioned event somewhere along the way that accelerated Logan's aging, yet somehow still left most of his healing factor intact?
It's possible that Logan's attempted suicide caused brain damage, limiting his healing factor to a certain extent.