* ExiledFromContinuity: In the first years and for most of its duration, the Ultimate universe was off-limits to crossovers with the main universe.
* MagnumOpusDissonance: When he was hired, Bendis (who only had experience in indie comics before this) did not thought that the Ultimate line would do very well. Not because of the project, but because of the context of Marvel Comics itself: back in 2000 there was no MCU (and no Spider-Man franchise in Sony, and the first X-Men film was about to be released), superheroes were completely unrelated with the tastes of teenagers and young adults, and Marvel was still nearing bankruptcy and trying to prove that WereStillRelevantDammit. He said that "When I got hired, I ''literally'' thought I was going to be writing one of the last — if not the last — Marvel comics"
* ScheduleSlip: Several titles have fallen victim to this, including ''Ultimates'' during vol. 1, ''New Ultimates'', and ''Ultimate X''. ''Ultimate Wolverine Vs. Hulk'' takes the cake, with ''four years'' passing between issues 2 and 3.
* WorkingTitle: Before settling for the "Ultimate" name for the inprint, the name "Ground Zero" was also considered.
** ''ComicBook/CivilWar'' was initially drafted by Millar as a story for the Ultimate universe. But the editors liked it so much that it was turned instead into a CrisisCrossover at the mainstream comics.
** Originally, Creator/GrantMorrison was going to pen an Ultimate Universe adaptation of The Kree-Srull War, which would have revealed the enemies the Chitauri were fleeing from in The Ultimates Volume 1 as The Kree and that the original Super-Soldier serum was made by Kree Scientists (who had been in hiding on Earth) from Chitauri DNA. However, Morrison returned to DC and this mini-series and the plot-lines it planned to introduce were thus abandoned.
** Before Creator/JephLoeb came aboard, Creator/MarkMillar planned to follow up The Ultimates Volume 2 with an ongoing series titled Ultimate Avengers, which would have detailed the original Ultimates team (now called by their mainstream name of The Avengers) operating independent from SHIELD out of Stark's New York townhouse. Millar later recycled story ideas he had for this series into the actual Ultimate Avengers series he would later pen.