Earth X/YMMV

Crowning Moment of Awesome: The main page quote. Black Bolt's swan song. Tony Stark buys the world more time. Reed's bravery and steadfastness. Basically, most of the whole series.
Epileptic Trees: The identity of the Daredevil from this continuity.
Hilarious in Hindsight: Thor is turned into a woman through Loki's meddling. Fast forward to 2010, and Loki is turned into a woman through Loki's meddling.

Critical Research Failure: Mephisto's plot to create alternate timelines actually makes sense; but Richmond's attempt to explain it badly garbles concepts of time and dimensionality.
Crowning Moment of Heartwarming: Reed's reunion with his wife.
Squick: "With the exception of a few opportunists who anticipated the coming need and secretly bred and sold animal life through the underground, Wakanda was the only known nation where mammal and fowl hasn't been hunted down and consumed. I still feel badly about Howard (the Duck)." The Skull had a roast fowl dinner when he first arrived at New York.

Crowning Moment of Heartwarming: Days of Future Past Wolverine hugs Paradise X Scott Summers.
They Wasted a Perfectly Good Plot: Well, more like they just couldn't, what with waning popularity and all. Colossus possessed the knowledge to bring a person back to life using Limbo. When Kurt asks Aaron why he never used it, Aaron answers; "Who says he didn't?"
- Also they never explored how Xen was formed. That would have been an interesting story.