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.
Although it was highlighted more in the tie-ins, while nearly every hero was MIA due to their own issues, Spider-Man was literally the only hero out saving lives from the destruction. Jonah Jameson saw this first hand.
Crowning Moment of Funny: An unintentional one. When the Thing goes to kill Doctor Doom, Doom asks "How did you get in here?" The artist and writer apparently weren't communicating properly, because we see the Thing coming through an open door.
Crowning Moment of Heartwarming: Hawkeye, despite disliking Hank Pym, decides to help him find Wasp because he knows how it is to lose a family member. The moment is genuinely touching, in contrast to its horrible conclusion.
Darkness-Induced Audience Apathy: The comic was so ridiculously dark that many readers either swore off the Ultimate continuity or were discouraged from getting into it.
Fridge Logic: Magneto uses his powers to open Cyclops' visor and shoot Wolverine. Why on Earth would Cyclops even have a metal visor, and why would he be stupid enough to wear it when he's knowingly going into battle AGAINST A GUY WITH MAGNETIC POWERS?
And for that matter why the Hell would Wolverine, the guy with the metal skeleton, charge straight at Magneto? And when the visor opened, why didn't Cyclops just close his eyes? And even more of a question, why were the heroes who are completely unaffected by Magneto's powers just standing around gawking like idiots while Wolverine is being fried alive? The only way this plot was possible was that the heroes were carrying the Idiot Ball like a lead weight the whole time.
How could Magneto activate Iron Man's force blast? Sure, his suit is made of metal, but Magneto's power lay in magetism - y'know, moving metal around. Not activating the suit's technologies.
A long standing problem with Magneto, as he's used his powers to reprogram sentinels in the past. In fact, he did so towards the climax of the very first Ultimate X-Men story arc, when the US government pulls the same "fight fire with gasoline" trick by sending an army of Sentinels into the Savage Land, which Magneto even lampshaded.
Idiot Plot: It actually takes 4 issues for the heroes to actually start acting like heroes. Not to mention the idea that the heroes literally stood back and did nothing while they watched Magneto rip Wolverine to shreds, killing him.
Narm: A lot. Probably the crowner is the above-mentioned moment where Doctor Doom demands to know how the Thing managed to open a door.
Never Live It Down: No matter how many good things he writes, Jeph Loeb will likely never escape the reputation gained from this comic.
Nightmare Fuel: Blob eating the Wasp's corpse. Unlike usual examples, however, this isn't considered a good thing in any way, even for fans who like being creeped out; as a matter of fact, most of them were just disgusted by it and thought even more this comic was going to suck.
Most of the deaths in this series count, but the one above is the most hideous example.