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!
I Knew It!: Issue #20 ends with the Reed Richards from the mainstream universe making contact, which would lead to a crossover. But, wait a moment. That would be the first crossover between the Ultimate and the mainstream universes... and it is not in a miniseries or Crisis Crossover of its own? There's not even any publicity about it? Many fans correctly guessed that the story would be something else.
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.
Narm: Even for Brian Bendis and / or Mark Millar, making Mole Man a man covered in moles called Arthur Molevik, rather than the regular Mole Man just being a short, blind man, is a ludicrous step too far.
Older Than They Think: The Fantastic Four had already appeared in Ultimate Marvel Team-Up, an issue that would be eventually ignored as an Early Installment Weirdness. Still, that version included two departures from the classic version that would be used by the ultimate version of the Ultimate Fantastic Four: they get their powers during an experiment involving the Negative Zone, and Sue is a capable and recognized scientist on her own right.
Arthur Molevik, a man working for a secretive government agency, deciding not only to continue working on a project after he'd been told not to, but to encrypt his files, the sort of thing that screams "HEY, I'M UP TO SOMETHING AND I DON'T WANT YOU TO KNOW". Surprise, he's quickly found out, and fired.
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.
If not in the present, then when he was a kid, Little Victor just needed a hug.