Ho Yay: Lampshaded when Ben and Reed go to face Thanos:
Oh, this is just pathetic. This laconic, heroic, tragicomic— garbage!!! Walking off to certain death with your heads held high! You might as well hold hands, because that's how homoerotic it is!
Moral Event Horizon: Reed begins his supervillain career by murdering his entire family. He follows up by trying to murder Sue. If he hadn't crossed it by then, his killing all the Asgardians in Ultimates sure did.
What an Idiot: It's the dramatic conclusion of the arc, and Reed Richards is squaring off against Nihil on the Vegas Strip! The tyrant opens his mouth to devour the hero, who stops him by picking up a nearby plasma rifle and wedging it in between his jaws! You'd expect: Nihil to do literally anything except what he actually does. Literally anything else. Instead: He tries to pull the gun out...by the trigger. It's... not pretty.
The Thing, even more than in the mainstream continuity; whereas mainstream Ben has long ago accepted his transformation and even embraced it, Ultimate Ben is so depressed by his transformation that he's attempted suicide. And each one fails because his body is nigh-invincible.