Board Thread:Questions and Answers/@comment-86191-20161025174807/@comment-4651179-20161025213735

The main difference is the amount of superhuman activity altogether. There are much fewer heroes (and gods and aliens) in the Ultimate Universe than there are in the Marvel Universe.

A much more specific yet notorious difference is the militarization of superheroes. In the Ultimate Universe, most "major players" are under governmental oversight. The Ultimates, Fantastic Four and the European Defense Initiative. The Ultimates became private for a while, but came back to the fold right after Ultimatum. Spider-Man (Parker) even started being trained by the Ultimates briefly before his apparent death.

S.H.I.E.L.D. is also much more involved in the superhero community and doesn't simply play Big Brother like its Marvel Universe counterpart does. They found and thawed Cap, assembled the Ultimates, created the Hulk, etc.